Method for rapid amplification of DNA

ABSTRACT

The present disclosure relates to methods of DNA amplification with a first primer that has a random sequence of nucleotides at its 3′ end and a generic sequence 5′ of the random nucleotides, as well as a second primer with the generic sequence of the first primer. The disclosure further relates to a method of precipitating DNA on a solid medium to improve DNA amplification. In a preferred embodiment, the presently disclosed methods are used for high-throughput genotyping of DNA samples, such as bloodstains or trace amounts of DNA.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

[0001] Not applicable.

REFERENCE TO A “MICROFICHE APPENDIX”

[0002] Not applicable.

BACKGROUND OF THE INVENTION

[0003] 1. Field of the Invention

[0004] The present disclosure relates generally to the field of DNAamplification and more particularly to the field of amplifying anystretch of DNA in a sequence-independent manner.

[0005] 2. Description of Related Art

[0006] The following description includes information that may be usefulin understanding the present disclosure. It is not an admission that anyof the information provided herein is prior art, or relevant, to thepresently claimed inventions, or that any publication specifically orimplicitly referenced is prior art.

[0007] It is well known that there is often an association betweengenetic variation and phenotype manifestation. Genetic variations andtheir associated phenotypes are studied using various methods ofgenotyping genomic DNA. A Single Nucleotide Polymorphism (SNP) is asingle nucleotide variation at a specific location in the genome ofdifferent individuals. SNPs are stable genetic variations frequentlyfound in genes, and contribute to the wide range of phenotypicvariations found in organisms. SNP genotyping is useful in developingdetailed genetic and physical maps of chromosomes. Genotyping denselydistributed SNP markers across the different chromosomes of anindividual can help reveal statistically significant correlationsbetween chromosomal loci and phenotypic expression. Extensivegenotyping, however, requires not only a simple and rapid way forobtaining, shipping, storing, and sorting large amounts of geneticmaterial, but also convenient and high-throughput methods for extractinglarge quantities of DNA from these samples.

[0008] There are a variety of available methods for obtaining andstoring tissue and/or blood samples. These alternatives allow tissue andblood samples to be stored and transported in a form suitable for therecovery of genomic DNA from the samples for genotype analysis. DNAsamples can be collected and stored on a variety of solid mediums,including Whatmann® paper, Guthrie cards, tubes, swabs, filter paper,slides, or other containers. When whole blood is collected on filterpaper, for example, it can be dried and stored at room temperature.

[0009] One known and more frequently used method for securing andstoring DNA is described in U.S. Pat. No. 5,496,562. This methodinvolves storing dried animal blood samples on chemically treated filterpaper, called FTA paper, that protects genomic DNA from degrading(commercially available as FTA™ paper by Whatmann®). FTA paper is lightweight and easy to store, which makes it a popular choice for collectinggenetic material and samples. Samples on FTA paper are convenientlystored and shipped at room temperature.

[0010] All of the materials available to those of skill in the art forstoring blood or other tissues containing DNA have limitations. Forexample, the amount of tissue or blood collected may be very limited,which makes wide-scale and high-throughput genotyping impractical andexpensive. For example, despite the widespread use of FTA paper, itsusefulness is limited because the stored bloodstains contain only asmall amount of genomic DNA. A 6.0 cm² piece of FTA paper only preservesapproximately 100 μl of blood, equivalent to approximately 1.0 μg ofDNA. While it is possible to extract genomic DNA from a larger piece ofFTA paper, the size of the paper makes it cumbersome to manipulate inthe small wells of a 96-well plate or a 384-well plate, both of whichare important tools for high-throughput screening of large numbers ofDNA samples. Therefore, the usefulness of a tool like FTA paper has beenrestricted to low-volume genotyping.

[0011] The limited amount of DNA stored on FTA paper also makes itimpractical for genotyping multiple polymorphisms and genetic loci in asingle organism. The FTA paper sample can be cut into smaller pieces forgenotyping multiple SNPs; a small circle of 1.0-2.0 mm² diameter of thesample contains about 1-5 ng of genomic DNA, which is sufficient for onepolymerase chain reaction (PCR). But this approach is undesirablebecause it requires repetitive cutting, sorting, and extracting of theFTA paper, which is not only tedious but also prone to human error. Fora genomic scan of hundreds or thousands of SNPs, the task of cutting andanalyzing DNA samples stored on FTA paper is an insurmountable barrierfor researchers.

[0012] Additionally, the strong adherence between DNA and FTA papermakes DNA extraction for analysis difficult. Although proteinase K andendonuclease digestion can facilitate DNA release as suggested by themanufacturer, this approach is too complicated and expensive forhigh-throughput operations. The commercially available FTA PurificationReagent, which can be used to prepare DNA stored on FTA paper foranalysis by PCR™ yields inconsistent results. For example, often nospecific DNA amplification is achieved after the DNA sample is processedusing this reagent, which is unacceptable in a high-throughputoperation. The manufacturer also suggests that the strong adhesion ofDNA to FTA paper allows for repeated genotyping of DNA stored on FTApaper. Notwithstanding the fact that PCR efficacy for “recycled” FTApaper has not been fully tested, cleaning the tiny FTA papers betweenconsecutive SNP PCRs is impractical for high-throughput processing. Thesmall pieces of floating filter paper are difficult to wash byconventional aspiration, and they tend to clog aspiration needles orpipette tips. Further, small pieces are easily lost during the cleaningprocess. Finally, repeated pipetting of PCR products has an associatedrisk of cross contamination among different wells.

[0013] The shortcomings associated with small samples of blood or tissuefrom an organism are overcome by efficient methods of whole genomic DNAamplification. For example, whole genomic DNA amplified from the smallamounts of DNA sample stored on FTA paper could be used in multiple PCRreactions to extensively genotype various polymorphisms such as SNPsfound in a single organism in a high-throughput screening process.Nevertheless, while several methods for whole genome amplification havebeen proposed and successfully used for various applications in thepast, these methods are generally inefficient, complex, and expensive.Therefore, the need exists for a simple and cost effective way ofamplifying genomic DNA from small samples of blood or tissue.

[0014] One of the first methods for amplifying DNA was the linkeradaptor-mediated PCR (LAM-PCR) approach, which has been applied tomicrodissected chromosomes (Zhou et al., Bio Techniques 28:766-774,2000; Albani et al., Plant J 4(5):899-903, November 1993), yeastartificial chromosome (YAC) DNA (Sutcliffe et al., Genomics13(4):1303-6, 1992), and genomic DNA (Kinzler et al., Nucleic Acids Res25:17(10):3645-53, May 1989). In this approach, the starting DNA isfirst digested with a restriction enzyme, usually an enzyme with a fourbase recognition sequence. After inactivation of the restriction enzyme,a known sequence (either an adaptor or a synthetic linker) is ligated tothe ends of the DNA fragments generated by the restriction-enzymedigest, providing primer binding sites for PCR amplification. The DNAcan then be amplified by PCR using primers that are complementary to thesequence of the adaptor or linker.

[0015] Unfortunately, the usefulness of LAM-PCR is limited because itinvolves multiple steps, including DNA fragmentation, adaptor or linkerligation, and PCR amplification. These steps make this process bothlaborious and expensive for high-throughput genotyping. An additionalshortcoming of this method is that sequences that do not contain therecognition sequence of the restriction enzyme used at appropriatelyspaced intervals will not be amplified by PCR because the regions willbe too long to amplify. This method is also time-consuming andcumbersome because of the extensive manipulations of DNA necessary toattach the known sequences to both ends of the fragments, especiallywhen applied to small quantities of DNA, such as microdissectedchromosomal pieces, or DNA found in bloodstains or small samples oftissue.

[0016] Another more restrictive method available for amplifying genomicDNA uses inter-ALU PCR (more generally known as inter-repetitive elementPCR), which relies on the presence of appropriately spaced and orientedALU repetitive elements or other repeated sequences. Inconsistentresults are obtained, however, with low complexity DNA sources such asYACs, cosmids, or phage, because of the low incidence of these repeatsequences. Other inconsistencies arise because repeated sequences do notoccur uniformly throughout the genome, and thus a sequence of interestoccurring in an area in which the necessary repeated sequences are rareor absent will not be amplified. Another major limitation of this methodis that it is species specific. For example, the use of this method isrestricted to DNA of the species from which the repetitive elements arederived and for which the PCR primers were constructed.

[0017] A method called degenerated oligonucleotide-primed PCR (DOP-PCR)utilizes partially degenerated sequence (6 out of 21) and repeatedthermocycling Telenius, et al., Genomics 13(3):718-25, 1992. In theDOP-PCR method, the first rounds of PCR amplification have a low primerannealing temperature of around 30° C. The primer used consists of arandom hexamer that is flanked on the 3′ side by a defined hexamer andon the 5′ side by a defined sequence. Because the 3′ end of the primerhas a defined hexamer, the target sequence must match this hexamer inorder to amplify. Therefore, the number of sequences that will beamplified by this method are limited. The inadequacy of the DOP-PCRmethod is further demonstrated when it is applied to DNA sources oflimited complexity such as YACs, cosmids, or phage inserts. Theresulting product is not a smear on a ethidium bromide stained agarosegel (as occurs with randomly amplified DNA), but rather distinct bands,indicating that hybridization occurs at relatively few sites and thussequence independent amplification is not achieved.

[0018] Another attempt to amplify genomic DNA was a method termedprimer-extension preamplification (PEP) (Zhang et al., Proc. Natl. Acad.Sci. USA 89:5847-5851, 1992). The PEP method utilizes 15 base pair (bp)random oligonucleotides and repeated thermocycling to randomly primemultiple sites in the genomic DNA for PCR. A method utilizing 6 basepair (bp) random oligonucleotides and PCR has also been reported (Penget al., Clin Pathol 47:605-608, 1994). Although both PEP and DOP-PCRhave been employed in several specific applications, they areconsistently hampered by their relatively low amplification efficiency(Wells et al., Nucleic Acids Res 27:1214-1218, 1999). A possibleexplanation for this low efficiency is that because the primers containrandom nucleotides and therefore form a large spectrum of differentoligonucleotides, the effective concentration of any specific primer isvery low, which may limit the exponential amplification of PCR.Additionally, the non-specific binding of the random oligonucleotidestends to initiate DNA synthesis within the PCR products of previousrounds. Therefore, the size of the PCR products decreases constantlywith each additional round of PCR amplification, which renders the finalPCR products very small, especially when a large number of PCR cyclesare performed. These small PCR products are not as useful as largerpieces of amplified DNA for the subsequent genetic analysis of the DNAor genotype analysis.

[0019] Another method of genomic DNA amplification, termed tagged randomPCR, was described by Grothues et al. (Nucleic Acids Res 21:1321-1322,1993) and Wong et al. (Nucleic Acids Res 24:3778-83, 1996). This methodattempts to overcome the shortcomings associated with PEP and DOP-PCR byseparating random priming and PCR amplification into two steps andamplifying whole genomic DNA with a single PCR primer. In the firstamplification step, tagged random primers consisting of a random 6 bp or9 to 15 bp 3′ tail and a constant 17 to 22 bp 5′ head indiscriminatelyprime the genomic DNA. Next, unincorporated tagged primers are removedby gel filtration using a Biogel P100 spin column or a Centricon-100spin column. In the second amplification step, the DNA molecules fittedwith the 5′ constant head and its reverse complement at both ends areamplified by PCR. Although the scheme can amplify whole genomic DNA, itsmultiple steps of reaction and purification are too complex andexpensive for high-throughput screening.

[0020] The construction of libraries from microdissected chromosomalbands is an elegant way to obtain DNA probes from genomic regions ofparticular interest. The applicability of this approach has beenrestricted by the time consuming and technically difficult process ofamplifying DNA from microdissected material. Traditionally, DNA from 20to 30 microdissected chromosomal bands is collected in a small droplet.The DNA is then subjected to various manipulations before it is used forPCR amplification. These manipulations include phenol/chloroformextractions, restriction enzyme digestion and ligation to a vector orlinker (LAM-PCR). These steps must be performed in very small volumes onthe stage of a microscope with specialized equipment (Kao et al., ProcNatl Acad Sci USA 1:88(5): 1984-8, 1991), which severely limits theusefulness of this technique.

[0021] Yeast artificial chromosomes (YACs) are ideal vectors for thedetailed mapping of large stretches of DNA. One of the maindisadvantages of the YAC cloning system is that there have been nomethods available to purify YAC DNA in large quantities. High molecularweight DNA can be prepared from yeast clones carrying YACs and the YACscan be isolated on a pulsed field gel. This approach, however, yieldsonly very small amounts of pure YAC DNA. This is a major disadvantagebecause many important uses of these large inserts, e.g. screening ofcDNA libraries or Fluorescent in situ hybridization (FISH) analysis,require larger amounts of purified YAC DNA.

[0022] Thus, a need exists for a more efficient and inexpensive methodfor amplifying DNA samples that is compatible with high-throughputscreening, is sequence independent, applicable to any type of DNA,useful for amplifying DNA from any species, and most important, capableof amplifying extremely limited amounts of DNA. There is also a need foran amplification process that is simple (to avoid the problem of PCRcontamination), has high fidelity in reproducing genetic material, andhas a low rate of distortion of amplified sequences.

BRIEF SUMMARY OF THE INVENTION

[0023] The present disclosure seeks to overcome the drawbacks inherentin other methods of DNA amplification by providing a simple and directmethod for amplifying DNA. The method of the present disclosurepreferably amplifies DNA in a sequence-independent manner using a singlereaction mixture and a single programmable thermocycling reaction. Thismethod can be used to amplify trace amounts of DNA, including genomicDNA from small tissue or blood samples, such as fine needle aspirates orsingle tissue sections, or even from a single cell. The single reactionmixture used in this method also greatly reduces the risk of samplecontamination and facilitates high-throughput screening, and in apreferred embodiment a single heat-stable DNA polymerase is included toamplify all DNA in the single reaction mixture. This method allows DNAto be amplified from any species or organism. It is understood that thepresent disclosure encompasses sequence independent amplification of DNAfrom any source, including but not limited to human, animal, plant,yeast, viral, eukaryotic, and prokaryotic DNA.

[0024] The present disclosure also offers an improved method forprocessing DNA samples on a solid medium. Other known methods ofpreparing DNA samples stored on a solid medium for genetic analysis orDNA amplification are inefficient and inconsistent, thereby limiting theusefulness of the information obtained from the DNA samples. The methodof the present disclosure seeks to overcome the drawbacks inherent inthese other methods by greatly simplifying the preparation of DNAsamples and improving the DNA for subsequent analysis. The method of thepresent disclosure precipitates the DNA sample on a solid medium usingmethods well known to those of skill in the art. In a preferredembodiment, the DNA sample is a bloodstain on a solid medium. The DNAprocessed according to the presently disclosed method can besubsequently subjected to DNA amplification using the presentlydisclosed methods and/or genetic analysis. This disclosed precipitationmethod produces more consistent results, reduces the cost ofhigh-throughput operations, and improves the quality of DNA amplifiedfrom the DNA sample.

[0025] The present disclosure includes methods of amplifying DNA from aDNA sample. In a preferred embodiment, the method of amplifying DNA usesa reaction mixture that contains a DNA sample; a first primer with arandom sequence of nucleotides at its 3′ end and a generic sequence 5′of the random nucleotides; and a second primer that has the genericsequence of the first primer but lacks the random sequence of the firstprimer. In a preferred embodiment, a single reaction mixture is used. Anexample of a first primer is the sequence designated SEQ ID NO: 1, andan example of the second primer is the sequence designated SEQ ID NO: 2.Preferably, the reaction mixture contains other components that arenecessary for DNA amplification, which are well known to those of skillin the art.

[0026] The DNA sample in the reaction mixture is subjected to DNAamplification by a first DNA polymerase, wherein the first primeranneals to the DNA to allow the first DNA polymerase to synthesize acomplementary DNA strand from the 3′ end of the first primer to producea DNA product. The steps for DNA amplification by the first DNApolymerase are denaturing the DNA product; annealing the first primerwith the DNA to allow the formation of a DNA-primer hybrid; andincubating the DNA-primer hybrid to allow the first DNA polymerase toextend the primer and synthesize the DNA product. Preferably, these DNAamplification steps are repeated at least one time. In a preferredembodiment, the annealing temperature and the incubating temperature arethe same. In another preferred embodiment, the DNA product produced bythe DNA amplification is flanked by the generic sequence and reversecomplement of the generic sequence.

[0027] This DNA product is then subjected to DNA amplification by aheat-stable DNA polymerase, wherein the second primer anneals to the DNAproduct and the heat-stable DNA polymerase synthesizes a complementaryDNA strand from the 3′ end of the second primer to produce a second DNAproduct. The steps for DNA amplification by the heat-stable DNApolymerase are denaturing the DNA product; annealing the second primerwith the DNA product to allow the formation of a DNA-primer hybrid; andincubating the DNA-primer hybrid to allow the heat-stable DNA polymeraseto synthesize the second DNA product. Preferably, these DNAamplification steps are repeated about 30 to about 35 times, and morepreferably about 40 times. In a preferred embodiment, the second DNAproduct is flanked by the generic sequence and the reverse complement ofthe generic sequence. In another preferred embodiment, the annealingtemperature is higher than the optimal annealing temperature of therandom sequence of nucleotides at the 3′ end of the first primer.

[0028] In a preferred embodiment, the first DNA polymerase has 5′ to 3′exonuclease activity or primer displacement activity. The first DNApolymerase is preferably E.coli DNA polymerase I, and the heat-stableDNA polymerase is preferably Taq DNA polymerase. In another preferredembodiment, the first DNA polymerase and the heat-stable DNA polymeraseare the same DNA polymerase, and that DNA polymerase is Taq DNApolymerase.

[0029] In another preferred embodiment, the first primer has about 4 toabout 8 random nucleotides at its 3′ end. In a more preferredembodiment, the first primer has about 6 random nucleotides at its 3′end. Preferably the generic sequence of the first primer is about 15 toabout 28 nucleotides in length, or more preferably about 20 to about 25nucleotides in length. The random nucleotides of the first primer mayalso be G:C rich or A:T rich, to preferably amplify certain regions ofthe DNA sample. Finally, the generic sequence of the first primerpreferably will have a single or multiple restriction enzyme recognitionsite, which will facilitate subcloning of the amplified DNA products.

[0030] In a preferred embodiment, the DNA sample is genomic DNA,microdissected chromosome DNA, yeast artificial chromosome (YAC) DNA,cosmid DNA, phage DNA, P1 derived artificial chromosome (PAC) DNA, orbacterial artificial chromosome (BAC) DNA. In another preferredembodiment, the DNA sample is mammalian DNA, plant DNA, yeast DNA, viralDNA, or prokaryotic DNA. In yet another preferred embodiment, the DNAsample is obtained from a human, bovine, porcine, ovine, equine, rodent,avian, fish, shrimp, plant, yeast, virus, or bacteria. Preferably theDNA sample is genomic DNA, wherein the method of amplifying DNA includesDNA amplification with a fluorescent label. In another preferredembodiment, the DNA sample is bovine DNA. Preferably, the DNA sample istissue on a solid medium, wherein the tissue is blood, preferably in theform of a bloodstain. In a preferred embodiment, the solid medium isfilter paper, wherein the filter paper is chemically treated, forexample FTA™ paper. In a preferred embodiment the bloodstain is from amammal, and the mammal is preferably human, bovine, or porcine. The DNAsample may be obtained from many sources well known to those of skill inthe art, including but not limited to a buccal swab, a nose swab, blood,cord blood, amniotic fluid, embryonic tissue, hair, endothelial cells,hoof clippings, or fingernail clipping.

[0031] In another preferred embodiment, the method of amplifying DNAfurther includes genotype analysis of the amplified DNA product.Alternatively, the method of amplifying DNA preferably further includesidentifying a single nucleotide polymorphism (SNP) in the amplified DNAproduct. In preferred embodiments, a SNP may be identified in the DNA ofan organism by a number of methods well known to those of skill in theart, including but not limited to identifying the SNP by DNA sequencing,by amplifying a PCR product and sequencing the PCR product, byOligonucleotide Ligation Assay (OLA), by Doublecode OLA, by Single BaseExtension Assay, by allele specific primer extension, or by mismatchhybridization. Preferably the identified SNP is associated with aphenotype, including disease phenotypes and desirable phenotypic traits.The amplified DNA generated by using the disclosed method of DNAamplification may also preferably be used to generate a DNA library,including but not limited to genomic DNA libraries, microdissectedchromosome DNA libraries, BAC libraries, YAC libraries, PAC libraries,cDNA libraries, phage libraries, and cosmid libraries.

[0032] Another aspect of the present disclosure is a preferred method ofamplifying DNA that uses a reaction mixture with a DNA sample; a firstprimer with a random sequence of nucleotides at its 3′ end and a genericsequence 5′ of the random nucleotides; a second primer with the genericsequence of the first primer and lacking the random sequence of thefirst primer; and a heat-stable DNA polymerase. In a preferredembodiment, a single reaction mixture is used. Preferably, the reactionmixture also contains other components that are necessary for DNAamplification, which are well known to those of skill in the art. In apreferred embodiment, the heat-stable DNA polymerase is Taq DNApolymerase, the DNA sample is a bloodstain on a solid medium, and theDNA sample is preferably dehydrated on the solid medium.

[0033] The DNA sample in the reaction mixture is subjected to DNAamplification wherein the first primer anneals to the DNA to allow theheat-stable DNA polymerase to synthesize a complementary DNA strand fromthe 3′ end of the first primer to produce a DNA product. The steps forDNA amplification by the heat-stable DNA polymerase are denaturing theDNA product; annealing the first primer with the DNA to allow theformation of a DNA-primer hybrid; and incubating the DNA-primer hybridto allow the heat-stable DNA polymerase to synthesize the DNA product.Preferably, these DNA amplification steps are repeated at least onetime. In a preferred embodiment, the annealing temperature and theincubating temperature are the same. In another preferred embodiment,the DNA product produced by the DNA amplification is flanked by thegeneric sequence and reverse complement of the generic sequence.

[0034] This DNA product is then subjected to DNA amplification by theheat-stable DNA polymerase, wherein the second primer anneals to the DNAproduct and the heat-stable DNA polymerase synthesizes a complementaryDNA strand from the 3′ end of the second primer to produce a second DNAproduct. The steps for DNA amplification by the heat-stable DNApolymerase are denaturing the DNA product; annealing the second primerwith the DNA product to allow the formation of a DNA-primer hybrid; andincubating the DNA-primer hybrid to allow the heat-stable DNA polymeraseto synthesize the second DNA product. Preferably, these DNAamplification steps are repeated about 30 to about 35 times, and morepreferably about 40 times. In a preferred embodiment, the second DNAproduct is flanked by the generic sequence and reverse complement of thegeneric sequence. In another preferred embodiment, the annealingtemperature is higher than the optimal annealing temperature of therandom sequence of the first primer.

[0035] In another preferred method of amplifying DNA, a reaction mixtureis provided that has a DNA sample, wherein the DNA sample is a tissue ona solid medium; a first primer with a random sequence of nucleotides atits 3′ end and a generic sequence 5′ of the random nucleotides; a secondprimer with the generic sequence of the first primer and lacking therandom sequence of the first primer; and a heat-stable DNA polymerase.In a preferred embodiment, a single reaction mixture is used. In apreferred embodiment, the tissue on the solid medium is blood. Inanother preferred embodiment the solid medium is filter paper, and thefilter paper is chemically treated. The DNA sample is preferablydehydrated on the filter paper. Preferably, the reaction mixture alsocontains other components that are necessary for DNA amplification,which are well known to those of skill in the art. In a preferredembodiment, the heat-stable DNA polymerase is Taq DNA polymerase, theDNA sample is a bloodstain on a solid medium, and the DNA sample ispreferably dehydrated on the solid medium.

[0036] The DNA sample in the reaction mixture is subjected to DNAamplification by a heat-stable DNA polymerase, wherein the first primeranneals to the DNA to allow the heat-stable DNA polymerase to synthesizea complementary DNA strand from the 3′ end of the first primer toproduce a DNA product. The steps for DNA amplification by theheat-stable DNA polymerase are denaturing the DNA product; annealing thefirst primer with the DNA to allow the formation of a DNA-primer hybrid;and incubating the DNA-primer hybrid to allow the heat-stable DNApolymerase to synthesize the DNA product. Preferably, these DNAamplification steps are repeated at least one time. In a preferredembodiment, the annealing temperature and the incubating temperature arethe same. In another preferred embodiment, the DNA product produced bythe DNA amplification is flanked by the generic sequence and reversecomplement of the generic sequence.

[0037] This DNA product is then subjected to DNA amplification by theheat-stable DNA polymerase, wherein the second primer anneals to the DNAproduct and the heat-stable DNA polymerase synthesizes a complementaryDNA strand from the 3′ end of the second primer to produce a second DNAproduct. The steps for DNA amplification by the heat-stable DNApolymerase are denaturing the DNA product; annealing the second primerwith the DNA product to allow the formation of a DNA-primer hybrid; andincubating the DNA-primer hybrid to allow the heat-stable DNA polymeraseto synthesize the second DNA product. Preferably, these DNAamplification steps are repeated about 30 to about 35 times, and morepreferably about 40 times. In a preferred embodiment, the second DNAproduct is flanked by the generic sequence and reverse complement of thegeneric sequence. In another preferred embodiment, the annealingtemperature is higher than the optimal annealing temperature of therandom sequence of nucleotides at the 3′ end of the first primer.

[0038] Another aspect of the present disclosure is a preferred method ofidentifying a polymorphism, which uses a reaction mixture with a DNAsample; a first primer with a random sequence of nucleotides at its 3′end and a generic sequence 5′ of the random nucleotides; and a secondprimer with the generic sequence of the first primer and lacking therandom sequence of the first primer. In a preferred embodiment, a singlereaction mixture is used. Preferably, the reaction mixture also containsother components that are necessary for DNA amplification, which arewell known to those of skill in the art. In a preferred embodiment, theamplified DNA products are analyzed to identify a polymorphism, andpreferably the polymorphism is a single nucleotide polymorphism (SNP).The methods of identifying SNPs are well known to those of skill in theart. In a preferred embodiment of identifying a SNP, the SNP isidentified by DNA sequencing, Oligonucleotide Ligation Assay (OLA),Doublecode OLA, Single Base Extension Assay, allele specific primerextension, or mismatch hybridization.

[0039] The DNA sample in the reaction mixture is subjected to DNAamplification by a first DNA polymerase, wherein the first primeranneals to the DNA to allow the first DNA polymerase to synthesize acomplementary DNA strand from the 3′ end of the first primer to producea DNA product. The steps for DNA amplification by the first DNApolymerase are denaturing the DNA product; annealing the first primerwith the DNA to allow the formation of a DNA-primer hybrid; andincubating the DNA-primer hybrid to allow the first DNA polymerase tosynthesize the DNA product. Preferably, these DNA amplification stepsare repeated at least one time. In a preferred embodiment, the DNAproduct produced by the DNA amplification is flanked by the genericsequence and reverse complement of the generic sequence.

[0040] This DNA product is then subjected to DNA amplification by aheat-stable DNA polymerase, wherein the second primer anneals to the DNAproduct to allow the heat-stable DNA polymerase to produce amplified DNAproducts. The amplified DNA products are produced when the heat-stableDNA polymerase synthesizes a complementary DNA strand from the 3′ end ofthe second primer annealed to the DNA product. The steps for DNAamplification by the heat-stable DNA polymerase are denaturing the DNAproduct; annealing the second primer with the DNA product to allow theformation of a DNA-primer hybrid; and incubating the DNA-primer hybridto allow the heat-stable DNA polymerase to synthesize the amplified DNAproducts. The amplified DNA products are then preferably analyzed toidentify a polymorphism. Preferably, these DNA amplification steps arerepeated about 30 to about 35 times, and more preferably about 40 times.In a preferred embodiment, the amplified DNA products are flanked by thegeneric sequence and reverse complement of the generic sequence. Inanother preferred embodiment, the annealing temperature is higher thanthe optimal annealing temperature of the random sequence of nucleotidesat the 3′ end of the first primer.

[0041] Another aspect of the present disclosure is a preferred method ofamplifying DNA that uses a reaction mixture with a DNA sample to beamplified; a first primer with a random sequence of nucleotides at its3′ end and a generic sequence 5′ of the random nucleotides; and a secondprimer with the generic sequence of the first primer and lacking therandom sequence of the first primer. Preferably, the reaction mixturealso contains other components that are necessary for DNA amplification,which are well known to those of skill in the art. In a preferredembodiment, the DNA sample is tissue on a solid medium, and the DNAsample is preferably dehydrated on the solid medium.

[0042] The DNA sample in the reaction mixture is heated to a temperaturethat denatures the DNA to be amplified, cooled to a temperature thatallows the random sequence of the first primer to hybridize to itscomplement DNA, and incubated to allow synthesis of a DNA product by aDNA polymerase. In a preferred embodiment the DNA polymerase is Taq DNApolymerase. Preferably, the steps of heating, cooling, and incubatingthe reaction mixture are repeated at least one time. In anotherpreferred embodiment, the DNA product is flanked by the generic sequenceand reverse complement of the generic sequence.

[0043] A series of DNA amplification reactions are performed with theDNA product, wherein the annealing step is at a temperature that selectsfor the generic sequence of the second primer hybridizing to complementDNA in the DNA product over the random sequence of the first primerhybridizing to complement DNA in the DNA product. Preferably, the DNAamplification reactions involve a heat-stable DNA polymerasesynthesizing a complementary DNA strand from the 3′ end of the secondprimer to produce amplified DNA products. The steps for DNAamplification by the heat-stable DNA polymerase are denaturing the DNAproduct; annealing the second primer with the DNA product to allow theformation of a DNA-primer hybrid; and incubating the DNA-primer hybridto allow the heat-stable DNA polymerase to synthesize amplified DNAproducts. Preferably, the series of DNA amplification reactions includesabout 30 to about 35 reactions, and more preferably about 40 reactions.In a preferred embodiment, the products of the DNA amplificationreactions are flanked by the generic sequence and reverse complement ofthe generic sequence.

[0044] A preferred embodiment of the present disclosure is a method ofamplifying a DNA sample on a solid medium that involves precipitatingthe DNA sample on the solid medium and subjecting the precipitated DNAto DNA amplification to produce amplified DNA products. Preferably thesolid medium is filter paper, and the filter paper is chemicallytreated. In a preferred embodiment, the DNA sample is dehydrated on thefilter paper. In another preferred embodiment, the DNA sample is tissue,and the tissue is blood.

[0045] The DNA sample on a solid medium is preferably precipitated withsalt and alcohol, and rinsed with alcohol. Preferably, the salt used toprecipitated the DNA is sodium acetate, potassium acetate, ammoniumacetate, sodium chloride, or potassium chloride; preferably the alcoholused is ethanol or isopropanol. In preferred embodiments, the producedamplified DNA products are subjected to genotype analysis, or apolymorphism is identified in the DNA products, preferably a singlenucleotide polymorphism (SNP). The SNP may be identified by a number oftechniques well known to those of skill in the art, including preferablyDNA sequencing, Oligonucleotide Ligation Assay (OLA), Doublecode OLA,Single Base Extension Assay, allele specific primer extension, ormismatch hybridization.

[0046] Another aspect of the present disclosure is a preferred method ofidentifying a polymorphism, which precipitates a DNA sample on a solidmedium, and uses a reaction mixture with the precipitated DNA sample; afirst primer with a random sequence of nucleotides at its 3′ end and ageneric sequence 5′ of the random nucleotides; and a second primer withthe generic sequence of the first primer and lacking the random sequenceof the first primer. In a preferred embodiment, a single reactionmixture is used. Preferably, the reaction mixture also contains othercomponents that are necessary for DNA amplification, which are wellknown to those of skill in the art. In a preferred embodiment, theamplified DNA products are analyzed to identify a polymorphism, andpreferably the polymorphism is a single nucleotide polymorphism (SNP).The methods of identifying SNPs are well known to those of skill in theart. In a preferred embodiment of identifying a SNP, the SNP isidentified by DNA sequencing, Oligonucleotide Ligation Assay (OLA),Doublecode OLA, Single Base Extension Assay, allele specific primerextension, or mismatch hybridization.

[0047] The DNA sample in the reaction mixture is subjected to DNAamplification by a first DNA polymerase, wherein the first primeranneals to the DNA to allow the first DNA polymerase to synthesize acomplementary DNA strand from the 3′ end of the first primer to producea DNA product. The steps for DNA amplification by the first DNApolymerase are denaturing the DNA product; annealing the first primerwith the DNA to allow the formation of a DNA-primer hybrid; andincubating the DNA-primer hybrid to allow the first DNA polymerase tosynthesize the DNA product. Preferably, these DNA amplification stepsare repeated at least one time. In a preferred embodiment, the DNAproduct produced by the DNA amplification is flanked by the genericsequence and reverse complement of the generic sequence.

[0048] This DNA product is then subjected to DNA amplification by aheat-stable DNA polymerase, wherein the second primer anneals to the DNAproduct to allow the heat-stable DNA polymerase to produce a second DNAproduct. The second DNA product is produced when the heat-stable DNApolymerase synthesizes a complementary DNA strand from the 3′ end of thesecond primer annealed to the DNA product. The steps for DNAamplification by the heat-stable DNA polymerase are denaturing the DNAproduct; annealing the second primer with the DNA product to allow theformation of a DNA-primer hybrid; and incubating the DNA-primer hybridto allow the heat-stable DNA polymerase to synthesize the second DNAproduct. The amplified DNA product is then preferably analyzed toidentify a polymorphism. Preferably, these DNA amplification steps arerepeated about 30 to about 35 times, and more preferably about 40 times.In a preferred embodiment, the second DNA product is flanked by thegeneric sequence and reverse complement of the generic sequence. Inanother preferred embodiment, the annealing temperature is higher thanthe optimal annealing temperature of the random sequence of nucleotidesat the 3′ end of the first primer.

[0049] In a preferred embodiment, the solid medium is filter paper, andthe filter paper is chemically treated. In another preferred embodiment,the DNA sample is dehydrated on the filter paper. Preferably, the DNAsample is tissue, and the tissue is blood. The DNA sample on a solidmedium is preferably precipitated with salt and alcohol, and rinsed withalcohol. Preferably, the salt used to precipitated the DNA is sodiumacetate, potassium acetate, ammonium acetate, sodium chloride, orpotassium chloride; preferably the alcohol used is ethanol orisopropanol.

[0050] The DNA amplification methods of the present disclosure will beuseful for amplifying small amounts of DNA, which will allow multiplesites in the DNA sample to be genotyped for high-throughput screening.Additionally, the present method will allow for the rapid constructionof band specific painting probes for any chromosomal region, and canalso be used to microdissect and amplify unidentifiable chromosomalregions or marker chromosomes in abnormal karyotypes. The presentlydisclosed method will also allow for the rapid cloning of amplified DNAfor sequencing or generating DNA libraries. Thus, the method will notonly be a valuable tool for genotype analysis and high-throughputscreening, it should also be a valuable tool in cytogenetic diagnosis.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

[0051] The following drawings form part of the present specification andare included to further demonstrate certain aspects of the presentdisclosure. The disclosure may be better understood by reference to oneor more of these drawings in combination with the detailed descriptionof specific embodiments presented herein.

[0052]FIG. 1. Diagram to illustrate the first set of reactions of theDNA amplification method. As demonstrated, during the first cycle of DNAamplification the sample DNA is denatured and the first primers randomlyprime the single-stranded DNA for DNA synthesis. The specific genericDNA sequence at the 5′ end of the first primer does not randomly annealto the DNA strand. Next, Taq DNA polymerase synthesizes thecomplementary DNA strand from the 3′ end of the randomly annealed firstprimers. In a second cycle of DNA amplification in the first set ofreactions, the newly synthesized DNA strand with the generic sequence atits 5′ end is denatured from the sample DNA strand. Next, the firstprimers again randomly prime the newly synthesized DNA strand, and TaqDNA polymerase synthesizes the complementary DNA strand from the 3′ endof the randomly annealed first primers. This results in a final productof a DNA strand flanked by the generic sequence at its 5′ end and thereverse complement of the generic sequence at its 3′ end. This DNAproduct will be amplified in a second set of reactions of DNAamplification using a second primer that hybridizes to the genericsequences flanking the DNA products.

[0053]FIG. 2. PCR amplification of DNA samples (bloodstains) stored onFTA paper. The efficiency of PCR amplification of samples processedusing the commercial FTA Purification Reagent is compared to samplesprocessed using a preferred method of the present disclosure. Identicalpunches obtained from the same bovine bloodstains on FTA paper weretreated using either the commercial FTA Purification Reagent or theprecipitation method of the present disclosure. After the DNA sampleswere treated, the samples were subjected to PCR amplification asdescribed in Example 1. Lane 1, DNA molecular size marker; lanes 2-5,direct PCR products of 4 bloodstain samples processed with commercialFTA Purification Reagent; lanes 7-10, direct PCR products of theidentical 4 bloodstain samples as lanes 2-5, respectively, firstprocessed with the precipitation method of the present disclosure. It isapparent that DNA samples processed using the precipitation method ofthe present disclosure are more consistently and optimally amplified byPCR than samples treated with FTA Purification Reagent.

[0054]FIG. 3. PCR products of bloodstains on FTA paper processed withthe precipitation method of the present disclosure were compared withPCR products of amplified genomic DNA generated from bloodstains on FTApaper using the precipitation method and the DNA amplification method ofthe present disclosure. Upper panel: Agarose gel electrophoresis ofbovine PCR products generated directly from bloodstains on FTA paperthat were processed with the precipitation method of the presentdisclosure. Lane 1, DNA molecular size marker; lanes 2-14, direct PCRproducts from the bloodstain samples of 13 individual animals. Lowerpanel: Agarose gel electrophoresis of bovine PCR products generatedusing genomic DNA amplified with the disclosed DNA amplification methodusing as DNA samples bloodstains on FTA paper that were processed withthe disclosed precipitation method. Lane 1, DNA molecular size marker;lanes 2-14, direct PCR products of DNA amplified from genomic DNAsamples of 13 individual animals. It is apparent that DNA amplified bythe method of the present disclosure can be used to accuratelycharacterize DNA samples by PCR.

[0055]FIG. 4. Genomic DNA amplification from bloodstains on FTA paper,comparing the commercial FTA Purification Reagent system with theprecipitation method of the present disclosure. Identical sets of DNAsamples were first processed using the commercial FTA PurificationReagent system or the presently disclosed precipitation method, and thenthe DNA samples were amplified using the DNA amplification method of thepresent disclosure. Lane 1, DNA molecular size marker; lanes 2-7,genomic DNA amplification of 6 bloodstains on FTA paper processed usingthe commercial FTA Purification Reagent; lanes 8-13, genomic DNAamplification of 6 bloodstains on FTA paper processed using theprecipitation method of the present disclosure. It is readily apparentthat the disclosed method of DNA amplification yields far more amplifiedgenomic DNA products when the disclosed precipitation method is used toprocess DNA samples on FTA paper than when the FTA Purification Reagentis used.

[0056]FIG. 5. Genomic DNA amplification of bloodstains stored on FTApaper using the presently disclosed DNA amplification method. Theefficiency of a series of generic DNA sequences used to generate a firstprimer and a second primer for amplifying genomic DNA were compared. Ineach of the reaction mixtures for DNA amplification with the secondprimers listed below, the first primer used contained the same genericsequence as the second primer with 6 additional random nucleotides atthe 3′ end. Lane 1, DNA molecular size marker; lane 2, genomic DNAamplification with a second primer having the sequence of SEQ ID NO: 3;lane 3, genomic DNA amplification with a second primer having thesequence of SEQ ID NO: 4; lane 4, genomic DNA amplification with asecond primer having the sequence of SEQ ID NO: 5; lane 5, genomic DNAamplification with a second primer having the sequence of SEQ ID NO: 6;lane 6, genomic DNA amplification with a second primer having thesequence of SEQ ID NO: 7; lane 7, genomic DNA amplification with asecond primer having the sequence of SEQ ID NO: 8; lane 8, genomic DNAamplification with a second primer having the sequence of SEQ ID NO: 9;lane 9, genomic DNA amplification with a second primer having thesequence of SEQ ID NO: 10; lane 10, genomic DNA amplification with asecond primer having the sequence of SEQ ID NO: 11; and lane 11, genomicDNA amplification with a second primer having the sequence of SEQ ID NO:12. The general ability of generic sequences designed according to thepresent disclosure to amplify DNA using the DNA amplification method isdemonstrated by the uniform DNA amplification demonstrated in lanes2-11.

[0057]FIG. 6. Diagram to illustrate the Doublecode OLA (oligonucleotideligation assay) reaction to detect SNP variations in a DNA sample. Theupper diagram illustrates one option for performing OLA using a labeledReporter oligonucleotide. The disadvantage of this technique is that aReporter oligonucleotide specific to a single SNP must be individuallylabeled by a fluor. Since a new labeled Reporter oligonucleotide must begenerated for each SNP genotyped, this method is an expensive option forlarge-scale genotyping. The lower diagram illustrates the Doublecode OLAreaction, which offers a significant improvement over the above methodbecause it uses a labeled generic AntiSignalcode oligonucleotide thatcan be produced in large quantities and utilized for detecting any SNP.This AntiSignalcode oligonucleotide is used with a Reporteroligonucleotide that contains the reverse complement of theAntiSignalcode (Signalcode sequence), as well as a region complementaryto a single SNP. Thus, this technique provides a less expensive optionfor detecting SNPs than the technique illustrated in the upper panel.

DETAILED DESCRIPTION OF THE INVENTION

[0058] Genetic analysis of limited quantities of genomic DNA oftenoccurs in the areas of DNA forensics, paleoarcheology, genetic diseasediagnosis, genetic linkage analysis, and genetic diversity analysis.Analysis and research in each of these areas will be greatly improved ifan efficient and inexpensive method for amplifying genomic DNA and othertypes of DNA samples in a sequence-independent matter is available. Moreextensive genetic analysis of small DNA samples using amplified genomicDNA offers a wide range of benefits in each of the above areas.Additionally, a method that could amplify genomic DNA from a singlecell, either haploid or diploid, would allow for a more complete geneticanalysis of an individual cell from, for example, a pre-implantationembryo, fetal cells in the peripheral blood of pregnant women, sperm, oroocytes. The methods of DNA amplification set forth in the presentdisclosure can be utilized in any of the above areas to amplify DNA fromlimited starting materials, thereby allowing for more complete geneticanalyses of a large range of DNA samples. Additionally, these methodsare practical for wide-scale, high-throughput screening of DNA samples.

[0059] Those of skill in the art understand that the basic steps in DNAamplification are heat denaturation, annealing of oligonucleotideprimers, and extension of complementary DNA by a DNA polymerase. Thesteps of denaturation, annealing, and extension make up a single cycleof DNA amplification. In the heat denaturation step, the temperature israised to a temperature sufficient to cause double-stranded DNA todenature into single-stranded DNA. Next, during the annealing step, thetemperature is lowered to a temperature that facilitates the annealingof the oligonucleotide primers to the single-stranded DNA. Finally,during extension, the incubation temperature allows the DNA polymeraseto synthesize complementary DNA from the 3′ end of the annealed primer.In the presently disclosed methods for DNA amplification, the sampleDNA, a first primer having random nucleotides at its 3′ end and ageneric sequence at its 5′ end, and a second primer with the genericsequence of the first primer are placed together in a single reactionmixture. The sample DNA is then amplified using a first set of reactionsand a second set of reactions, each of which includes the steps ofdenaturation, annealing, and extension.

[0060] The first set of reactions of DNA amplification begins bydenaturing the double-stranded DNA sample to a single-strandedcondition, which allows primers to anneal to the DNA. Next, the reactiontemperature is lowered to a temperature that allows the randomnucleotides at the 3′ end of the first primer to anneal to the DNA toform hybrid duplexes. After the hybrid duplexes form, DNA polymerasepresent in the reaction mixture extends the complementary DNA strandfrom the 3′ end of the first primer during an incubation period. The DNApolymerase will preferably have 5′ to 3′ exonuclease activity so that itwill be able to remove other first primers annealed further downstreamon the same DNA strand, thus allowing longer complementary DNA strandsto be synthesized during the first set of reactions. Alternatively, theDNA polymerase can have primer displacement activity, which will achievea similar result. Primer displacement activity means that when the DNApolymerase is moving along the DNA strand synthesizing complementary DNAand it encounters another primer annealed to the DNA, the primer will bedisplaced and the polymerase reaction will proceed. This activity alsoresults in longer polymerization products. While the annealing andincubation steps are preferably performed at different temperatures,both the annealing and incubation steps may occur at the sametemperature if the DNA polymerase is active at that temperature in thefirst set of reactions.

[0061] After the first cycle of DNA amplification described above, thenewly synthesized complementary DNA strand will have the genericsequence of the first primer at its 5′ end, which was incorporated intothe strand when the 3′ end of the first primer was used as the startingpoint for synthesizing the complementary DNA strand (see FIG. 1.). Theabove steps of denaturation, annealing, and extension can be repeated,and generally should be repeated at least once during the first set ofreactions. The denaturation step of the second cycle of the first set ofreactions separates the new first cycle DNA strands with the 5′ genericsequence from the original DNA strands. After denaturation, the newfirst cycle DNA strands are available to the first primer present in thereaction mixture for another round of annealing and extension.

[0062] During the second cycle of the first set of reactions, the firstprimer anneals to the first cycle DNA strand, DNA polymerase extends acomplementary strand from the 3′ end of the first primer, and the newlysynthesized complementary DNA once again incorporates the 5′ end of thefirst primer into its sequence. This new second cycle DNA fragment willalso have the reverse complement of the generic sequence on its 3′ end,because DNA polymerase will synthesize the full-length complementary DNAproduct of the first cycle DNA strand, which has the generic sequence atits 5′ end. Thus, the DNA fragments amplified during the first set ofreactions have the generic sequence at one end of the fragment and itsreverse complement at the other. These DNA products of the first set ofreactions flanked with the generic sequence and its reverse complementcan now be readily amplified during a second set of reactions with asecond primer. The second primer has the same generic DNA sequence asthe first primer, but without the random nucleotides at its 3′ end.

[0063] The DNA products of the first set of reactions are subsequentlyamplified using the second primer present in the single reactionmixture. After these DNA products are denatured, the temperature of thereaction is lowered so that the second primer will anneal to the genericsequence at the ends of the DNA products. The annealing temperature usedfor the second set of reactions will generally be higher than theannealing temperature used in the first set of reactions. The annealingtemperature used in the second set of reactions should be higher thanthe optimal annealing temperature of the random sequence of thenucleotides of the first primer. The higher temperature will minimize orprevent random priming by the first primer through its random nucleotidesequence located at its 3′ end in the second set of reactions. Thischaracteristic eliminates the need to remove any remaining first primerfrom the single reaction mixture during the second set of reactions.

[0064] After the second primer anneals to the ends of the DNA products,a heat-stable DNA polymerase extends the complementary DNA strand fromthe 3′ end of the second primer. The second set of reactions involvesrepeating the above steps of denaturation, annealing, and extension toachieve exponential amplification of the DNA products, preferably usinga total of about 30 to about 40 cycles. The final amplified DNA is readyfor extensive analysis using a variety of techniques, such as utilizingthe amplified DNA to genotype multiple sites in the DNA, includingpolymorphisms such as SNPs, single tandem repeats (STRs), restrictionfragment length polymorphisms (RFLPs), variable number of tandem repeats(VNTRs), complex tandem repeats (CTRs), microsatellites, deletions,substitutions, or insertions. Alternatively, the amplified DNA may beused to generate DNA libraries from a variety of sources.

[0065] Any type of DNA sample may be amplified using the methods of thepresent disclosure because it is a sequence-independent method of DNAamplification that can amplify even trace amounts of DNA. In onepreferred embodiment, the DNA sample is genomic DNA, microdissectedchromosome DNA, yeast artificial chromosome (YAC) DNA, P1 derivedartificial chromosome (PAC) DNA, cosmid DNA, phage DNA, or bacterialartificial chromosome (BAC) DNA. In another preferred embodiment, theDNA sample is tissue, blood, or a single cell. Preferably the DNA sampleis readily and easily obtained from an organism, and is easy to store.The DNA sample can be obtained from any species or organism, includingbut not limited to human, mammal, bovine, porcine, ovine, equine,rodent, avian, fish, zebrafish, shrimp, plants, yeast, virus, orbacteria.

[0066] DNA samples of tissue or blood containing genomic DNA suitablefor DNA amplification by the disclosed method may be convenientlyobtained from, for example, buccal swab, nose swab, hair, mouthwash,cord blood, amniotic fluid, embryonic tissue, endothelial cells, hoofclippings, or fingernail clipping. Genomic DNA in paraffin-embeddedtissue may also be amplified using the disclosed method. The DNAamplification methods of the present disclosure can amplify genomic DNAfrom a single cell, including but not limited to a single cell isolatedfrom a pre-implantation embryo, fetal cells in the peripheral blood ofpregnant women, sperm, or oocytes, or a single cell from any tissue. Asingle cell may be isolated using a variety of methods, including flowcytometry (Herzenberg et al., Proc Natl Acad Sci USA 76:1453-55, 1979;Iverson et al., Prenatal Diagnosis 1:61-73, 1981; Bianchi et al.,Prenatal Diagnosis 11:523-28, 1991), which can utilize fluorescentactivation cell sorting (FACS), magnetic-activated cell sorting (MACS,Ganshirt-Ahlert et al., Am J Obstet Gynecol 166:1350, 1992), or acombination of both procedures. Additionally, a combination of gradientcentrifugation and flow cytometry methods can also be used to increaseisolation or sorting efficiency. In one preferred embodiment, the DNAsample does not have to be purified or treated with proteinase K beforeDNA amplification using the disclosed method.

[0067] The first primer used in the DNA amplification methods of thepresent disclosure preferably has about 4 to about 9 random nucleotidesat its 3′ end. In a preferred embodiment, the first primer has 5, 6, 7,or 8 random nucleotides at its 3′ end. The first primer also has fromabout 10 to about 30 and preferably from about 15 to about 25nucleotides of a generic sequence at its 5′ end. In a preferredembodiment the first primer has 16, 17, 18, 19, 20, 21, 22, 23, or 24nucleotides of a generic sequence at its 5′ end. The random sequence ofnucleotides and the generic sequence 5′ of the random nucleotides may beadjacent in the first primer. Alternatively, one or more nucleotides maybe inserted between the random sequence of nucleotides and the genericsequence 5′ of the random nucleotides in the first primer. The firstprimer may also have additional nucleotides 5′ of the generic sequence.An example of a first primer is the sequence designated SEQ ID NO: 1, inwhich N designates a random nucleotide. The random sequence ofnucleotides can be composed of any of the nucleotides, for example G, A,T, or C, in any order. It is understood that these letter designationsrepresent G for guanine, A for adenine, T for thymine, and C forcytosine nucleotides. The random nucleotides can also include nucleotideanalogs, and other modified nucleotides that are well known to those ofskill in the art.

[0068] The first primer theoretically may contain all combinations ofthese nucleotides in every position of the random portion of the primer.Thus, the random nucleotides at the 3′ end of the first primer will becomplementary to random sites throughout the target DNA segments. It isunderstood by those of skill in the art that the longer the randomsequence of nucleotides is in the first primer the less often the targetsequence will occur in the genome, and therefore the less often thefirst primer will anneal to the target DNA segments. Additionally, therandom sequence of the first primer can be designed to be rich in thenucleotides A and T or alternatively in the nucleotides G and C to allowfor preferential amplification of particular regions in the sample DNA,such as A:T rich regions or G:C rich regions. It is well within theskill of those in the art to use any ratio of the 4 nucleotides togenerate the random sequence of nucleotides.

[0069] As an example, if the 3′ end of the first primer has 5 randomnucleotides, there would be 4⁵ or 1,024 different sequences in therandom segment of the first primer for that particular amplification.The complements of these sequences occur in both orientations at randomthroughout the denatured DNA segments of the DNA sample. By bothorientations it is meant that priming would occur on both strands of themelted DNA duplex that is to be amplified.

[0070] As used herein, the term “generic sequence” refers to any DNAsequence that would be a useful DNA amplification primer. An example ofthe second primer is the sequence designated SEQ ID NO: 2. Thus, thegeneric sequence will preferably not have any obvious self-homologies,nor runs of the same nucleotide, and the generic sequence is preferablynot overly G:C or A:T rich. A primer that contains self-homologies orsequences in one region that are complementary to sequences in anotherregion of the primer will form internal hairpin duplexes and thus wouldbe unavailable to hybridize with the sample DNA. Also, since G:C pairinginvolves 3 hydrogen bonds and A:T pairing involves 2 hydrogen bonds, aprimer with a disproportionately high content of the nucleotides G or C,singly or in combination, will have a higher melting temperature than aprimer that was comprised of a higher content of A and T. One of skillin the art can use this characteristic to manipulate the annealingtemperatures of the first and second primers to a higher or lowertemperature in the disclosed DNA amplification method. Within the limitsmentioned above, any generic sequence that can be used to amplify DNAusing the disclosed method is contemplated to be within the scope of thepresent disclosure.

[0071] The sequence of the second primer used in the second set ofreactions is the same as the generic nucleotide sequence 5′ of therandom nucleotide sequence of the first primer. While the second primermay have additional nucleotides at its 5′ end, this will affect theannealing temperature of the DNA amplification reaction. The secondprimer may also have additional nucleotides at its 3′ end, but these mayinterfere with the ability of the primer to uniformly amplify DNAproducts during the second set of reactions of DNA amplification byreducing the ability of the second primer to universally bind andamplify the DNA products of the first set of reactions. Therefore, thesecond primer-will preferably have no additional nucleotides on its 3′end.

[0072] In the first set of reactions of the disclosed method asdescribed in the paragraphs above, lower temperatures for the annealingreaction are used because the first primer anneals to the sample DNAthrough a short sequence of random nucleotides at its 3′ end. Theincubation temperature preferably will allow for DNA polymerase tosuccessfully synthesize the complementary DNA strand from the 3′ end ofthe annealed primer. If Taq DNA polymerase is used in the first set ofreactions, an extension temperature that allows Taq to have polymeraseactivity should be used. The DNA products of this first set of reactionsare flanked by the generic sequence of the first primer and its reversecomplement.

[0073] During the second set of reactions of DNA amplification, thesecond primer will hybridize to these flanking sequences. Because thegeneric DNA sequence is longer than the stretch of random nucleotides atthe 3′ end of the first primer, the annealing temperature in the secondset of reactions will generally be at a higher temperature. The higherannealing temperature will generally minimize or prevent any remainingfirst primers that were not incorporated into DNA products of the firstset of reactions but are still present in the reaction mixture fromannealing to the DNA products and randomly initiating DNA synthesis.Higher temperatures generally require the use of a polymerase that isheat-stable, which means that the polymerase can synthesize DNA at hightemperatures. One well-known example of a heat-stable DNA polymerase isTaq DNA polymerase. A number of heat-stable or thermostable DNApolymerases are commercially available, including recombinant Taq DNApolymerases and native Taq DNA polymerases (see Table 2). Another optionis to use long-range PCR to generate longer DNA products with, forexample, TaqPlus DNA Polymerase. Long-range PCR can be used in eitherthe first set of reactions, the second set of reactions, or both sets ofreactions. In one embodiment, Tub DNA polymerase can be used to amplifylong DNA sequences in the presently disclosed DNA amplification method.Protocols for using Tub DNA polymerase and amplifying long regions ofDNA are found in Forrester and Redford (Methods Mol. Biol. 67:31-38,1997), incorporated herein by reference.

[0074] In the presently disclosed method, the DNA to be amplified in thefirst set of reactions is first denatured by heating the reactionmixture to between about 90° C. and about 100° C., and preferably toabout 95° C. for about one to about five minutes and preferably forabout two minutes. During this step, both the first and second primersare present in the reaction mixture. Alternatively, the second primermay be added to the reaction mixture after the first set of reactionsbut before the second set of reactions. The first and second primers canbe added to the reaction mixture containing the DNA sample to beamplified before heat denaturation or at any time during thedenaturation step of the first cycle of the first set of reactions. Inthe preferred embodiment, the first and second primers are added to thesingle reaction mixture in equal molar ratios. The molar ratios of thetwo primers, however, may also vary in relation to each other tooptimize DNA amplification. The molar ratios of the DNA to be amplifiedand the first and second primers can be varied by one of skill in theart to optimize DNA amplification.

[0075] Next, the temperature of the reaction mixture is lowered to atemperature that allows the first primer to anneal to thesingle-stranded DNA. The second primer present in the reaction mixturewill not generally anneal to the single-stranded DNA in the first set ofreactions because the reverse complement of the longer generic DNAsequence necessary for annealing the primer will rarely, if at all, bepresent in the single-stranded DNA. The annealing temperature of therandom sequence of nucleotides of the first primer preferably should bebetween about 37° C. and about 50° C., preferably between about 42° C.and about 45° C. Preferably, a different temperature from the annealingtemperature may be used during the incubation period for extension ofthe complementary DNA strand that allows the DNA polymerase tosynthesize DNA from the 3′ end of the first primer. If the DNApolymerase functions at the annealing temperature, then this temperaturemay be maintained during the incubation period. The incubation period ispreferably about 2 minutes to about 7 minutes, more preferably about 5minutes.

[0076] These steps of the first set of reactions should be repeated atleast once, so that preferably two cycles of these initial DNAamplification steps are performed, although more than two cycles of DNAamplification in this first set of reactions is contemplated. Forexample, 3 or 4 cycles may be performed in the first set of reactions.But for every additional cycle of denaturation, annealing, andextension, the DNA products available for the second set of reactions ofDNA amplification will generally be shortened. This is because eachsuccessive round of random priming by the first primer further shortensthe previously amplified DNA products. This effect is overcome duringthe second set of reactions of DNA amplification because the secondprimers anneal to the ends of the DNA products flanked by the genericsequence and the reverse complement of the generic sequence produced inthe first set of reactions.

[0077] The DNA products of the first set of reactions, which are flankedby the generic sequence and its reverse complement are subsequentlyexponentially amplified in the second set of reactions of DNAamplification in the disclosed method. In the second set of reactions,the DNA products of the first set of reactions are first denatured byheating the reaction mixture to between about 90° C. and about 100° C.,and preferably to about 95° C. for about 15 seconds to about 2 minutes,preferably for about 30 seconds to about 1 minute. Next, the temperatureof the reaction mixture is decreased to a temperature that allows thesecond primer to anneal to the single stranded DNA products. Theannealing temperature of the second primer is preferably between about55° C. and about 68° C., preferably between about 60° C. and about 65°C. The annealing temperature of the second primer must be stringentenough to minimize or prevent random priming by the unincorporated firstprimers remaining in the reaction mixture. Therefore, it is notnecessary to remove the first primers from the reaction mixture duringthe second set of reactions, which increases the efficiency of thedisclosed method. This also greatly simplifies the present DNAamplification method for high-throughput screening as compared to otherknown methods.

[0078] While the incubation temperature may be the same as the annealingtemperature in the second set of reactions if the DNA polymerase isactive at that temperature, preferably the temperature of the incubationstep is raised to a more optimal temperature for the heat-stable DNApolymerase to synthesize DNA. The optimal temperature for the extensionstep will be dependent on the DNA polymerase used in the second set ofreactions. For example, during the incubation step of the second set ofreactions, the temperature is increased to about 68° C. to about 75° C.,and preferably to about 70° C. to about 72° C., and held for about 30seconds to about 10 minutes, and preferably for about 4 minutes to about6 minutes. The denaturation, annealing, and extension steps of thesecond set of reactions are repeated about 30 to about 40 times, andpreferably about 33 to about 35 times. The reaction can then be held atabout 72° C. for about 7 minutes to about 10 minutes to complete anynascent polymerizations. It is not necessary to add fresh enzyme aftereach denaturation step if a heat-stable DNA polymerase such as the TaqDNA polymerase is used because Taq is not completely denatured by thedenaturation step, and functions optimally at higher temperatures.Although a non-heat-stable DNA polymerase could also be used in thesecond set of reactions if it were added after each denaturation step ofevery cycle, this inefficient method would be impractical forhigh-throughput screening.

[0079] It is well known to those of skill in the art that the optimaltemperatures for each step of the first set of reactions and the secondset of reactions are determined (usually empirically) by the size of thesample DNA to be amplified and by the size and sequence of the primers.For example, simple formulas for determining the melting temperature ofa perfectly matched duplex based on the G:C content of the primer arewell known in the art. The optimal annealing temperature of a primer canbe calculated by one of skill in the art by using a variety of availablecomputer software programs, such as Oligo Analyzer, which is availableat the website www.idtdna.com. It is also well known to one of skill inthe art that the temperatures between any of the steps in the first setof reactions and/or the second set of reactions may be increased ordecreased gradually over about a 1 to about an 8 minute period of time,and preferably over about a 3 minute period of time.

[0080] One of skill in the art may also desire to incorporate one ormore restriction enzyme sites in the generic sequence for subsequentcloning of the amplified products. Restriction enzymes sites are DNAsequences that are recognized and cleaved at a specific point by arestriction endonuclease enzyme. The use of particular restrictionenzymes is well known in the art (see Table 1), and a particularrestriction enzyme compatible with the vector of choice for cloning theamplified DNA may be chosen. The number of available vectors are toonumerous to list, and are well known to those of skill in the art.Popular vectors such as pBR322, or the pGem or PUC series of plasmids,contain certain specific restriction enzyme recognition sites in theirpolyclonal regions. The generic sequence can be designed so that one ormore recognition sequences are included in the generic primer that arecompatible with sites in the chosen cloning vector.

[0081] In a certain embodiment, the present disclosure encompasses afirst primer and a second primer for use in DNA amplification. The firstprimer preferably has a region of about 4 to about 8 random nucleotidesat its 3′ end and about 15 to about 25 bp of a generic DNA 5′ of therandom nucleotide sequence. This first primer is further characterizedby the ability of its random sequence of nucleotides to hybridize to DNAsequences at a temperature of between about 37° C. and about 42° C. Thesecond primer is preferably between about 15 and about 25 bp in length,and has the same sequence as the generic sequence 5′ of the randomsequence of nucleotides in the first primer. The second primer may alsohave additional nucleotides to facilitate the method of DNAamplification, particularly in relation to the high stringency annealingstep in the second set of reactions. The second primer can furthercontain a restriction enzyme recognition site to facilitate thesubcloning of the amplified DNA products into a vector of choice or astretch of CUA repeats to facilitate cloning, for example by the “CloneAmp” protocol (BRL).

[0082] In a preferred embodiment, the DNA polymerase used to amplify theDNA in the first set of reactions is the same as the heat-stable DNApolymerase used in the second set of reactions. Using the same DNApolymerase for both the first and second set of reactions greatlysimplifies the disclosed method of DNA amplification because only onereaction mixture is prepared with the single heat-stable DNA polymerase,which greatly facilitates high-throughput screening. Using the same DNApolymerase means that the enzyme is simply added to the initial reactionmixture, and no additional enzyme must be added during the first orsecond set of reactions of DNA amplification.

[0083] It is also contemplated, however, that one DNA polymerase may beused in the first set of reactions and a second heat-stable DNApolymerase used in the second set of reactions. During the first set ofreactions, if a heat-stable DNA polymerase is not used, fresh enzymemust be added to the reaction mixture after each denaturation step,because the DNA polymerase will be destroyed by the heat necessary todenature the DNA. The DNA amplification steps of the first set ofreactions are repeated one to three times, preferably one time asdiscussed above, again with fresh enzyme added after each denaturationstep. A heat-stable DNA polymerase must then be added for the second setof reactions of DNA amplification, either before, during or after thefirst denaturation step of the second set of reactions.

[0084] The preferred DNA polymerase used in the presently disclosedmethod is a heat-stable enzyme with 5′ to 3′ exonuclease activity, oralternatively primer displacement activity. For example, Taq DNApolymerase can be added to the initial reaction mixture to amplify theDNA in both the first set of reactions and the second set of reactionsof the disclosed method. Taq DNA polymerase possesses intrinsic 5′ to 3′exonuclease activity, which allows Taq to digest oligonucleotide primersthat it encounters downstream while synthesizing complementary DNA(Longley et al., Nucleic Acids Res 18(24):73 17-22, 1990). DNApolymerases that may be used in the first set of reactions include anypolymerase with 5′ to 3′ exonuclease activity, or alternatively primerdisplacement activity with or without exonuclease activity. Enzymes thatmay be used in the first set of reactions include but are not limitedto, Taq DNA polymerase, modified Taq DNA polymerase such as for exampleAmplitaq Gold, E.coli DNA Polymerase I, Tub DNA Polymerase, and DNAPolymerase I (see Table 2).

[0085] If the DNA polymerase used in the first set of reactions differsfrom the heat-stable DNA polymerase used in the second set of reactions,the final DNA products of the first set of reactions may have to bediluted into buffer that allows the heat-stable DNA polymerase toperform optimally. The first set of reactions may be performed inrelatively low volume, particularly when the sample DNA is present insmall amounts as in microdissected chromosomes and in YACs isolated frompulsed field gels, or from small tissue or blood samples, or singlecells. It is contemplated that the volume of the first set of reactionsand the second set of reactions may vary widely depending on theparticular application and that higher or lower reaction volumes areencompassed by the present disclosure. Although a small aliquot of thefirst set of reactions may be used with a heat-stable DNA polymerase andits buffer in the second set of reactions, preferably the reactionvolume for both the first set of reactions and second set of reactionsis the same, particularly if the same DNA polymerase is utilized forboth sets of reactions.

[0086] It is contemplated that when DNA polymerase and its buffer areadded to the single reaction mixture of the present method, othercomponents necessary for DNA amplification are present in the reactionmixture. The necessary reaction components for DNA amplification arewell known to those of skill in the art and may include, but are notlimited to, bovine serum albumin, MgCl₂ in a concentration of about 1.5mM to about 5 mM final concentration, the four deoxynucleotide bases(dATP, dGTP, dTTP, and dCTP), and purified water, for example distilled,deionized or ultrafiltered water. The buffers employed may containcomponents such as Tris HCl at a pH of about 7.0 to about 9.0, MgCl₂,NaCl, and DTT (dithiothreitol). Buffers may also include KCl andgelatin. The composition of buffers for PCR and DNA amplification arewell known to those of skill in the art, and the concentration ofcertain components such as MgCl₂ for example, can easily be determinedempirically for each reaction.

[0087] It is also understood by those of skill in the art that thetemperatures, incubation periods, and ramp times of the DNAamplification steps may vary considerably without significantly alteringthe efficiency of DNA amplification and other results. Alternatively,those of skill in the art may altery these parameters to optimize theDNA amplification reactions. These minor variations in reactionconditions and parameters are included within the scope of the presentdisclosure. The DNA products of the above reactions may be visualized byrunning them on an agarose or acrylamide electrophoresis gel, preferablyon a 1.5% to 2.0% agarose gel. After staining the gel with ethidiumbromide, the products of the random, sequence independent amplificationwill preferably appear as a smear.

[0088] In one embodiment, the present disclosure encompasses a methodfor amplifying DNA, independent of the sequence of the DNA, thatincludes the steps of:

[0089] (a) adding to the DNA sample in a single reaction mixture, 10 mMTris HCl (pH 8.3), 5 mM MgCl₂, 50 mM KCl, 0.001% gelatin, 300 μM dNTP(dATP, dGTP, dCTP, and dTTP), 300 nM of the first primer having thesequence of SEQ ID NO: 1, 300 nM of the second primer having thesequence of SEQ ID NO: 2, and 1.25 unit Taq DNA polymerase, for a totalvolume of about 50 μM;

[0090] (b) denaturing the DNA by heating the reaction mixture to atemperature of about 95° C. for about 5 minutes;

[0091] (c) denaturing the DNA by heating the reaction mixture to atemperature of about 95° C. for about 1 minute, and then cooling thereaction mixture to a temperature of about 42° C. for about 5 minutes,thereby allowing the first primer to anneal to the denatured DNA to forma DNA-primer hybrid and the Taq DNA polymerase to synthesize thecomplementary strand of DNA from the 3′ end of the first primer;

[0092] (d) repeating step (c) one time;

[0093] (e) denaturing the DNA products by heating the reaction mixtureto a temperature of about 95° C. for about 15 seconds, cooling thereaction mixture to a temperature of about 65° C., thereby allowing thesecond primer to anneal to the denatured DNA to form a DNA-primerhybrid; and raising the reaction mixture to a temperature of about 68°C., thereby allowing the Taq DNA polymerase to synthesize thecomplementary strand of DNA from the 3′ end of the second primer;

[0094] (f) repeating step (e) about 39 times.

[0095] An example of the first primer is the sequence5′-TAGCAGTGGTAACAACGCAGAGANNNNN-3′ (SEQ ID NO: 1). An example of thesecond primer is the sequence 5′-TAGCAGTGGTAACAACGCAGAGA-3′ (SEQ ID NO:2). Additional examples of the generic sequence that may be used as asecond primer in the presently disclosed method to amplify DNA include,but are not limited to: 5′-ACAACGCAGAGTAAGCAGTGGTA-3′; SEQ ID NO:35′-ACAACGGTAGCAGAGTAAGCAGT-3′; SEQ ID NO:45′-GAGTAAGCAGTACAACGGTAGCA-3′; SEQ ID NO:55′-GAGGCATAAGCAGTACAACGGTA-3′; SEQ ID NO:65′-CAACGGTAGAGGCATAAGCAGTA-3′; SEQ ID NO:75′-GGCATAAGCAGTACAACGGTAGA-3′; SEQ ID NO:85′-AACGGTAGAGGCATAAGCAGTAC-3′; SEQ ID NO:95′-AGTACAACGGTAGAGGCATAAGC-3′; SEQ ID NO:105′-AAGCAGTACAACGGTAGAGGCAT-3′; SEQ ID NO:115′-CGGTAGAGGCATAAGCAGTACAA-3′. SEQ ID NO:12

[0096] The first primer used in the same reaction mixture for DNAamplification with each of the above second primers will contain thesame generic sequence with an additional random sequence of nucleotidesat its 3′ end. The optimal annealing temperatures of the first set ofreactions and the second set of reactions of DNA amplification can bedetermined by one of skill in the art based on the generic DNA sequenceand the number of random nucleotides at the 3′ end of the first primer.Preferably, the optimal annealing temperature of each set of reactionswill be such that second primer annealing is minimized or prevented inthe first set of reactions and first primer annealing through its randomsequence of nucleotides is minimized or prevented in the second set ofreactions.

[0097] When DNA samples utilized in the presently disclosed DNAamplification methods are stored on a solid medium, preparing the DNAsample for amplification and/or genetic analysis can be not onlyinefficient, but also can yield inconsistent results, thereby limitingthe information that is obtained from the DNA sample. The presentdisclosure seeks to overcome the drawbacks inherent in other methods ofpreparing DNA samples stored on solid mediums for DNA amplificationand/or genetic analysis. The presently disclosed method, also termed theprecipitation method, greatly simplifies the preparation of DNA samplesstored on a solid medium by eliminating the unnecessary steps of DNApurification. In the disclosed method, the DNA sample on a solid mediumis precipitated by methods well known to those of skill in the art, andthen directly subjected to DNA amplification and/or genetic analysis.This method produces more consistent results, reduces the cost ofhigh-throughput operations, and improves the quality of DNA amplifiedfrom the DNA sample.

[0098] The present disclosure includes the variety of solid mediums wellknown to those of skill in the art for storing DNA, including as tissueand blood samples. Preferably, the solid medium is dry, and has a solidmatrix or solid support, such as preferably an absorbent cellulose-basedpaper (such as filter paper), or a micromesh of synthetic plasticsmaterials. The solid matrix may also be in the form of a tablet orpellet. Preferably the solid medium will protect against the degradationof the DNA sample incorporated or absorbed on the matrix or support. Asolid medium allows DNA samples to be stored and transported in a formsuitable for the recovery of the DNA in the sample for genotypeanalysis. DNA samples can be collected and stored for example on FTA™paper, Whatmann® paper, Gibson paper, Guthrie cards, swabs, and filterpaper. In a preferred embodiment the DNA sample is stored on FTA paper.Blood or tissue collected on filter paper can be dried and stored atroom temperature.

[0099] Methods of precipitating DNA using a salt and alcohol solutionare well known to those of skill in the art, and are included within thescope of the present disclosure. In a preferred embodiment, theprecipitation method of the present disclosure begins by washing the DNAsample on the solid medium with water, for example distilled, deionized,or ultrafiltered water, to remove any chemicals that might interferewith subsequent DNA amplification reactions. In a preferred embodiment,the DNA sample is repeatedly washed with water. Next, the solid mediumis treated with a solution that includes salt and alcohol, whichprecipitates the DNA in the sample. After the precipitation step the DNAis fixed on the solid support. In a preferred embodiment, the salt usedto precipitate the DNA is sodium acetate, potassium acetate, or ammoniumacetate, preferably at a concentration of about 0.1 to about 0.5 M, morepreferably about 0.2 to about 0.3 M. In another preferred embodiment,the alcohol used to precipitate the DNA is isopropanol, ethanol, orother similar water-miscible solvents such as n-propanol, preferably ata purity level of about 70% to about 100%, more preferably about 95%. Itis well within the skill ofthose in the art to determine the appropriateratio of salt to alcohol in the precipitation solution to precipitatethe DNA. In a preferred embodiment, the ratio is 50/50 v/v.

[0100] After the DNA is precipitated, it is washed with alcohol todissolve any salts remaining in the sample from the precipitation step.This step can also accelerate dehydration of the sample. In a preferredembodiment, the alcohol used to wash the precipitated DNA isisopropanol, ethanol, or other similar water-miscible solvents such asn-propanol, preferably at a purity level of about 80% to about 95%, morepreferably about 70%. Interestingly, when DNA samples on FTA paper areprocessed using the disclosed precipitation method, the final DNA-papercan remain the red-brown color of blood. Nevertheless, the processed DNAon the FTA paper now can be efficiently and predictably amplified by anyone of many methods of DNA amplification known by those of skill in theart, including but not limited to the DNA amplification method of thepresent disclosure, as well as PCR™. Thus, the presently disclosedmethods greatly reduce the variation of DNA amplification efficiencyfound when DNA samples stored on solid supports are processed usingcommercially available reagents.

[0101] Additionally, the solutions used in the presently disclosedprecipitation method, which include water, alcohol, and salts, areinexpensive and easy to make. The disclosed precipitation method thusalso greatly reduces the cost of high-throughput operations,particularly when compared to other commercially available reagents. Forexample, the ethanol wash can reduce the time for FTA paper dehydrationby at least 50% when compared to the water-based FTA PurificationReagent protocol. Additionally, the presently disclosed methods forprecipitation and DNA amplification to analyze DNA samples stored on FTApaper can all be conducted in 96-well or 384-well plates, which greatlyfacilitates high-throughput operations.

[0102] Genotype analysis of sample DNA on a solid support, processedusing the disclosed precipitation and/or DNA amplification methods, orgenotype analysis of DNA amplified by the preferred methods of thepresent disclosure, may be performed using a variety of methods andtechniques that are well known to those of skill in the art. Theadvantages offered by the disclosed methods of DNA amplification forhigh-throughput screening are that the genotypes of large numbers oforganisms can be rapidly screened for diagnostic or research purposes.The term “genotype analysis” refers to any type of genetic typing,genotyping, fingerprinting, haplotyping, DNA typing, or any similarphrase. The term includes the use of any methods or protocols known tothose of skill in the art for determining an individual's genotype atone or more genetic loci, including identifying haplotypes. Techniquesthat are nucleic acid based include but are not limited to sizefractionation, SNP analysis, allele specific oligonucleotide (ASO)hybridization, sequencing, RFLP analysis, denaturation temperatureanalysis, and mass spectrometry analysis. Methodologies available tothose of skill in the art are numerous and continually developing, andcannot be detailed herein. Many types of polymorphisms may be detectedusing amplified DNA, including but not limited to SNPs, RFLPs, VNTRs,STRs, CTRs, and microsatellites.

[0103] Single nucleotide polymorphisms (SNPs) are nucleotide sequencevariants that are of predictive value in identifying many geneticdiseases, as well as phenotypic characteristics that may be desirable,which are often caused by a limited number of different mutations in apopulation. SNPs are found in both coding and non-coding regions ofgenomic DNA. In spite of the paucity of scorable phenotypes, SNPs arefound in large numbers throughout the human genome (Cooper et al., HumGenet 69:201-205, 1985). Certain SNPs result in disease-causingmutations such as, for example, heritable breast cancer (Cannon-Albrightand Skolnick, Semin Oncol 23:1-5, 1996). It is specifically contemplatedthat DNA amplified by the disclosed methods may be useful in thedetection of SNPs or other polymorphisms in an individual. Currentmethods of screening for polymorphisms are known (see for example U.S.Pat. Nos. 6,221,592 and 5,679,524). A limitation of these techniques,however, is the inability to provide multiple copies of genomic DNA toenhance signals and facilitate detection. The disclosed methods overcomethis problem by facilitating rapid, high-throughput DNA amplification ofrandomly primed nucleic acid sequences throughout the full length of,for example, an individual's genome. Since multiple copies of eachregion including a SNP or other polymorphism would be present in asample following DNA amplification using the disclosed methods, thelikelihood of producing a detectable signal utilizing standard SNPdetection methods increases.

[0104] A SNP may be identified in the DNA of an organism by a number ofmethods well known to those of skill in the art, including but notlimited to identifying the SNP by PCR™ or DNA amplification,Oligonucleotide Ligation Assay (OLA) (Landegren et al., Science241:1077, 1988), Doublecode OLA, mismatch hybridization, massspectrometry, Single Base Extension Assay, RFLP detection based onallele-specific restriction-endonuclease cleavage (Kan and Dozy, Lancetii:910-912, 1978), hybridization with allele-specific oligonucleotideprobes (Wallace et al., Nucl Acids Res 6:3543-3557, 1978), includingimmobilized oligonucleotides (Saiki et al., Proc Natl Acad Sci USA86:6230-6234, 1989) or oligonucleotide arrays (Maskos and Southern, NuclAcids Res 21:2269-2270, 1993), allele-specific PCR™ (Newton et al., NuclAcids Res 17:2503-16, 1989), mismatch-repair detection (MRD) (Faham andCox, Genome Res 5:474-482, 1995), binding of MutS protein (Wagner etal., Nucl Acids Res 23:3944-3948, 1995),single-strand-conformation-polymorphism detection (Orita et al.,Genomics 5:874-879, 1983), RNAase cleavage at mismatched base-pairs(Myers et al., Science 230:1242, 1985), chemical (Cotton et al., ProcNatl Acad Sci USA 85:4397-4401, 1988) or enzymatic (Youil et al., ProcNatl Acad Sci USA 92:87-91, 1995) cleavage of heteroduplex DNA, methodsbased on allele specific primer extension (Syvanen et al., Genomics8:684-692, 1990), genetic bit analysis (GBA) (Nikiforov et al., NuciAcids Res 22:4167-4175, 1994), and radioactive and/or fluorescent DNAsequencing using standard procedures well known in the art.

[0105] Preferably the identified SNP is linked to a phenotype, includingdisease phenotypes and desirable phenotypic traits. The amplified DNAproducts of the disclosed methods may also be used to generate a DNAlibrary, including genomic DNA libraries, particularly if the genericsequence of the first and second primers include a restriction enzymesite to facilitate cloning of the DNA products. Additionally, thepresently disclosed methods allow for the rapid construction of bandspecific painting probes for any chromosomal region, and can also beused to microdissect and amplify unidentifiable chromosomal regions ormarker chromosomes in abnormal karyotypes. Thus, the disclosed methodsare not only a valuable tool for genotype analysis and high-throughputscreening, but also a valuable tool in cytogenetic diagnosis.

[0106] A Single Base Extension Assay is performed by annealing anoligonucleotide primer to a complementary nucleic acid, and extendingthe 3′ end of the annealed primer with a chain terminating nucleotidethat is added in a template directed reaction catalyzed by a DNApolymerase. The selectivity and sensitivity of a single base primerextension reaction are affected by the length of the oligonucleotideprimer and the reaction conditions (e.g. annealing temperature, saltconcentration). The selectivity of a primer extension reaction reflectsthe amount of exact complementary hybridization between anoligonucleotide primer and a nucleic acid in a sample. A highlyselective reaction promotes primer hybridization only to nucleic acidswith an exact complementary sequence (i.e. there are no base mismatchesbetween the hybridized primer and nucleic acid). In contrast, in a nonselective reaction, the primer also hybridizes to nucleic acids with apartial complementary sequence (i.e. there are base mismatches betweenthe hybridized primer and nucleic acid). In general, parameters whichfavor selective primer hybridization (for example shorter primers andhigher annealing temperatures) result in a lower level of hybridizedprimer. Therefore, parameters which favor a selective single base primerextension assay result in decreased sensitivity of the assay.

[0107] Additionally, cycled Single Base Extension Reactions may beperformed by annealing a nucleic acid primer immediately 5′ to a regioncontaining a single base to be detected. Two separate reactions areconducted. In the first reaction, a primer is annealed to thecomplementary nucleic acid, and labeled nucleic acids complementary tonon-wild-type variants at the single base to be detected, and unlabeleddideoxy nucleic acids complementary to the wild-type base, are combined.Primer extension is stopped the first time a base is added to theprimer. Presence of label in the extended primer is indicative of thepresence of a non-wild-type variant. A DNA polymerase, such asSequenase™ (Amersham), is used for primer extension. In a preferredembodiment, a thermostable polymerase, such as Taq or thermal sequenaseis used to allow more efficient cycling. Once an extension reaction iscompleted, the first and second probes bound to target nucleic acids aredissociated by heating the reaction mixture above the meltingtemperature of the hybrids. The reaction mixture is then cooled belowthe melting temperature of the hybrids and additional primer ispermitted to associate with target nucleic acids for another round ofextension reactions. After completion of all cycles, extension productsare isolated and analyzed. Alternatively, chain-terminating methodsother than dideoxy nucleotides may be used. For example, chaintermination occurs when no additional bases are available forincorporation at the next available nucleotide on the primer.

[0108] A particularly powerful means of analyzing genetic informationfrom DNA amplified using the disclosed methods is DNA chip technology.DNA chips and microarrays comprising arrays of oligonucleotide orpolynucleotide probes can be used to determine whether a target nucleicacid has a nucleotide sequence identical to or different from a specificreference sequence. The basic chip or microarray encompasses an array ofoligonucleotide or polynucleotide probes immobilized on a solid support.Chips for screening and detection are designed to contain probesexhibiting complementarity to one or more selected sequences whosesequence is known. Chips are used to read a target sequence comprisingeither the reference sequence itself or variants of that sequence.Target sequences may differ from the reference sequence at one or morepositions but show a high overall degree of sequence identity with thereference sequence (e.g., at least 75, 90, 95, 99, 99.9, or 99.99%).Hybridization of a target sequence to an immobilized probe results in adetectable signal. Signal can be delivered for example by conformationalchanges occurring in the probe, quenching or excitation of a labelincorporated into the bound probe, or by quenching or excitation of alabel incorporated into the target. Signal delivery may be readmanually, mechanically, or digitally. A number of patents, hereinincorporated by reference, disclose the preparation and use of DNA chipsand microarrays including: U.S. Pat. Nos. 5,837,832, 6,156,501,6,174,683, and 5,985,567. Additionally, allele specific primer extensioncan be combined with primer arrays for high-throughput genotyping ofSNPs (see Pastinen et al., Genome Res 10(7):1031-42, 2000, incorporatedherein by reference).

[0109] In the context of the present disclosure, it is specificallycontemplated that the DNA amplification products of the disclosedmethods may be analyzed using DNA chips or microarrays in order todetect specific genetic sequences, including genetic polymorphisms ormutations, such as for example SNPs. In one embodiment, it is envisionedthat genomic DNA will be amplified utilizing the methods of the presentdisclosure in order to produce a library of DNA sequences theoreticallyencompassing the entire genomic sequence. The amplified DNA products maythen be passed over a DNA chip or microarray encompassingoligonucleotide or polynucleotide probes. The ability or inability ofthe amplified DNA to hybridize to the microarray or DNA chip willfacilitate the characterization of the specific sequences and theirpolymorphisms present in the DNA sample.

[0110] One embodiment of the present disclosure involves fluorescence insitu hybridization (FISH) analysis of chromosomes. First, a chromosomalDNA sample of interest is obtained. This sample may be a YAC chromosomalinsert, a sample of microdissected chromosome, a cosmid DNA insert, aPAC DNA insert, a plasmid insert, or a phage insert, for example lambdaphage. For example, YAC DNA may be isolated from the other yeastchromosomes on a pulsed field electrophoresis gel. Once obtained, theDNA is amplified by the disclosed method. The amplified DNA can then belabeled by a further PCR that contains a labeled nucleotide base whichwill be incorporated into the amplified product. Using PCR to label DNAis well known to those of skill in the art. The label may include, butis not limited to, biotin, Spectrum-Orange, or Spectrum-Green. Using thedisclosed method for amplifying DNA, no prior purification of the DNA isrequired, and the method results in a substantial improvement in thespeed of probe preparation and in the quality of the FISH signal overother DNA amplification strategies. The ability to obtain such reliableFISH signals will allow new ways of screening for the presence of commontranslocations in a variety of human tumors.

[0111] Additionally, labeled amplified DNA can be hybridized to achromosome preparation such as interphase or, preferably, metaphasespreads. In metaphase spreads, the chromosomes are shortened andthickened and are more easily visualized and identified. Hybridizationwith the labeled probe allows one to determine the particular chromosomeand the position on the chromosome from which the amplified probe wasderived. Amplified, labeled DNA may also be hybridized to interphasenuclei in order to determine the number of hybridization sites in thenucleus. The hybridized probes that are labeled with biotin can bevisualized with fluorescein-isothiocyanate conjugated avidin under afluorescence microscope. Probes labeled with Spectrum-Orange orSpectrum-Green are directly visualized by fluorescence microscopy.

[0112] The methods and preferred embodiments of the present disclosurehave been described above. Many techniques and methods are well known tothose of skill in the art and may be used to assist practitioners incarrying out the methods of the present disclosure. The following is ageneral description of some of these techniques.

[0113] Nucleic Acids:

[0114] Genes are sequences of DNA in an organism's genome encodinginformation that is converted into various products making up a wholecell. They are expressed by the process of transcription, which involvescopying the sequence of DNA into RNA. Most genes encode information tomake proteins, but some encode RNAs involved in other processes. If agene encodes a protein, its transcription product is called mRNA(“messenger” RNA). After transcription in the nucleus (where DNA islocated), the mRNA is transported into the cytoplasm for the process oftranslation, which converts the code of the mRNA into a sequence ofamino acids to form protein. In order to direct transport of mRNA intothe cytoplasm, the 3′ ends of mRNA molecules are post-transcriptionallymodified by the addition of several adenylate residues to form the“polyA” tail. This characteristic modification distinguishes geneexpression products destined to make protein from other molecules in thecell, and thereby provides one means for detecting and monitoring thegene expression activities of a cell.

[0115] 1. Oligonucleotide Probes and Primers:

[0116] Nucleic acid sequences that are “complementary” are those thatare capable of base-pairing according to the standard Watson-Crickcomplementary rules. That is, the larger purines will base pair with thesmaller pyrimidines to form combinations of guanine paired with cytosine(G:C) and adenine paired with either thymine (A:T) in the case of DNA,or adenine paired with uracil (A:U) in the case of RNA. Inclusion ofless common bases such as inosine, 5-methylcytosine, 6-methyladenine,hypoxanthine and others in hybridizing sequences does not interfere withpairing. As used herein, the term “complementary” sequences meansnucleic acid sequences that are substantially complementary, as may beassessed by the same nucleotide comparison set forth above, or asdefined as being capable of annealing to the nucleic acid segment beingdescribed under relatively stringent conditions such as those describedherein.

[0117] The term primer, as defined herein, is meant to encompass anynucleic acid that is capable of priming the synthesis of a nascentnucleic acid in a template-dependent process. Sequence specific primersshould be of sufficient length to provide specific annealing to thetargeted RNA or DNA sequence. The use of a primer of between about 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,62, 63, 64, 65, 66, 67, 68, 69, 70, 75, 80, 85, 90, 95, and 100 or morenucleotides in length allows the formation of a duplex molecule that isboth stable and selective, although shorter and longer primers arespecifically contemplated in the context of the present disclosure. Forinitial DNA amplification steps, hybridization of as few as 5 to 9nucleotide bases is contemplated. Complementary sequences over stretchesgreater than 20 bases in length are generally preferred for subsequentamplification steps, in order to increase stability and selectivity ofthe hybrid, and thereby improve the quality and degree of particularhybrid molecules obtained.

[0118] Although shorter primers are easier to make and increase in vivoaccessibility, numerous other factors are involved in determining thespecificity of hybridization. Both binding affinity and sequencespecificity of a primer to its complementary target increases withincreasing length. It is contemplated that exemplary primers of 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,62, 63, 64, 65, 66, 67, 68, 69, 70, 75, 80, 85, 90, 95, and 100 or morenucleotide base pairs will be used, although others are contemplated aswell. Accordingly, nucleotide sequences may be selected for theirability to selectively form duplex molecules with complementarystretches of genes, DNA, or RNAs, or more specifically to provideprimers for amplification of DNA or RNA preparations including DNA orRNA directly or indirectly derived from cells, cell lysates, andtissues. Probes and primers of the present disclosure are used toamplify DNA, as well as detect genes, changes in gene expression, genepolymorphisms, single nucleotide polymorphisms, and changes in mRNAexpression where one could be detecting virtually any gene or genes ofinterest from any species. The target polynucleotide will be RNAmolecules, mRNA, cDNA, DNA, or amplified DNA. By varying the stringencyof annealing, and the region of the primer, different targets may bediscovered.

[0119] Primers may be chemically synthesized by methods well knownwithin the art. Chemical synthesis methods allow for the placement ofdetectable labels such as fluorescent labels, radioactive labels, etc.to be placed virtually anywhere within the polynucleic acid sequence.Solid phase methods as well as other methods of oligonucleotide orpolynucleotide synthesis known to one of ordinary skill may used withinthe context of the disclosure.

[0120] It is specifically contemplated that a wide variety ofappropriate detection or recognition means are known in the art and maybe incorporated into the primers. Such labels may include, but are notlimited to: fluorescent labels, radioactive labels, mass labels,affinity labels, chromophores, dyes, electroluminescence,chemiluminescence, enzymatic tags, or other ligands, such asavidin/biotin, or antibodies, which are capable of being detected andare described below.

[0121] 2. DNA Amplification:

[0122] One of the best known amplification methods is PCR™, which isdescribed in detail in U.S. Pat. Nos. 4,683,195, 4,683,202 and4,800,159, each incorporated herein by reference. While PCR™ isconsidered to be an acceptable means of carrying out DNA amplification,it is specifically contemplated that the methods of the presentdisclosure may be carried out using alternate amplification techniqueswhich would be well known to one of ordinary skill and are brieflydiscussed below. In PCR™, pairs of primers that selectively hybridize tonucleic acids are used under conditions that permit selectivehybridization. The term primer, as used herein, encompasses any nucleicacid that is capable of priming the synthesis of a nascent nucleic acidin a template-dependent process. Primers may be provided indouble-stranded or single-stranded form, although the single-strandedform is preferred. The primers are used in any one of a number oftemplate dependent processes to amplify the target-gene sequencespresent in a given template sample.

[0123] The nucleic acid target for the disclosed DNA amplificationmethod is generally considered to be any nucleic acid or nucleic acidanalog capable of being amplified by techniques well known in the art.By way of example, target nucleic acids specifically contemplated in thecontext of the disclosure, may include, but is not limited to: genomicDNA, cDNA, RNA, mRNA, cosmid DNA, BAC DNA, PAC DNA, YAC DNA, andsynthetic DNA. In a contemplated embodiment, genomic DNA is from aprokaryotic or eukaryotic cell or tissue and utilized as the sample DNAin the disclosed DNA amplification method. In other embodiments, poly-AmRNA is isolated and reverse transcribed (referred to as RT) to obtaincDNA, which is then used as the sample DNA for DNA amplification usingthe presently disclosed method. In other contemplated embodiments, cDNAmay be obtained and used as the sample DNA to be amplified. In stillanother embodiment, RNA or mRNA is directly amplified using thedisclosed DNA amplification method, wherein the starting material is anRNA sample rather than a DNA sample.

[0124] i. PCR™

[0125] In PCR™ two primer sequences are prepared which are complementaryto regions on opposite complementary strands of the target-gene(s)sequence. The primers will hybridize to form a DNA:primer hybrid if thetarget-gene(s) sequence is present in a sample. An excess ofdeoxyribonucleoside triphosphates are added to a reaction mixture alongwith a DNA polymerase, e.g., Taq polymerase, that facilitatestemplate-dependent nucleic acid synthesis.

[0126] If the DNA:primer hybrid is formed, the polymerase will cause theprimers to be extended along the target-gene(s) sequence by adding onnucleotides. By raising and lowering the temperature of the reactionmixture, the extended primers will dissociate from the target-gene(s) toform reaction products, excess primers will bind to the target-gene(s)and to the reaction products and the process is repeated. These multiplerounds of amplification, referred to as “cycles,” are conducted until asufficient amount of amplification product is produced.

[0127] Next, the amplification product is detected. In certainapplications, the detection may be performed by visual means.Alternatively, the detection may involve indirect identification of theproduct via fluorescent labels, chemiluminescence, radioactivescintigraphy of incorporated radiolabel or incorporation of labelednucleotides, mass labels or even via a system using electrical orthermal impulse signals.

[0128] ii LCR

[0129] Another method for amplification is the ligase chain reaction(“LCR”), disclosed in European Patent Application No. 320,308,incorporated herein by reference. In LCR, two complementary probe pairsare prepared, and in the presence of the target sequence, each pair willbind to opposite complementary strands of the target such that theyabut. In the presence of a ligase, the two probe pairs will link to forma single unit. By temperature cycling, as in PCR™, bound ligated unitsdissociate from the target and then serve as “target sequences” forligation of excess probe pairs. U.S. Pat. No. 4,883,750, incorporatedherein by reference, describes a method similar to LCR for binding probepairs to a target sequence.

[0130] iii. Qbeta Replicase

[0131] Qbeta Replicase, described in PCT Patent Application No.PCT/US87/00880, also may be used as still another amplification methodin the present disclosure. In this method, a replicative sequence of RNAwhich has a region complementary to that of a target is added to asample in the presence of an RNA polymerase. The polymerase will copythe replicative sequence which can then be detected.

[0132] iv. Isothermal Amplification

[0133] An isothermal amplification method, in which restrictionendonucleases and ligases are used to achieve the amplification oftarget molecules that contain nucleotide 5′-[α-thio]-triphosphates inone stand of a restriction site also may be useful in the DNAamplification. Such an amplification method is described by Walker etal. (Nucleic Acids Res 20(7):1691-6, 1992), incorporated herein byreference.

[0134] v. Strand Displacement Amplification

[0135] Strand Displacement Amplification (SDA) is another method ofcarrying out isothermal amplification of nucleic acids which involvesmultiple rounds of strand displacement and synthesis, i.e., nicktranslation. The SDA technique is described in U.S. Pat. Nos. 5,712,124,5,648,211 and 5,455,166, herein incorporated by reference. A similarmethod, called Repair Chain Reaction (RCR), involves annealing severalprobes throughout a region targeted for amplification, followed by arepair reaction in which only two of the four bases are present. Theother two bases can be added as biotinylated derivatives for easydetection. A similar approach is used in SDA.

[0136] vi. Cyclic Probe Reaction

[0137] Target specific sequences can also be detected using a cyclicprobe reaction (CPR). In CPR, a probe having 3′ and, 5′ sequences ofnon-specific DNA and a middle sequence of specific RNA is hybridized toDNA that is present in a sample. Upon hybridization, the reaction istreated with RNase H, and the products of the probe identified asdistinctive products are released after digestion. The original templateis annealed to another cycling probe and the reaction is repeated.

[0138] vii. Transcription-Based Amplification

[0139] Other nucleic acid amplification procedures specificallycontemplated in the context of the present disclosure includetranscription-based amplification systems (rAS), including nucleic acidsequence based amplification (NASBA) and 3SR, Kwoh et al., Proc NatlAcad Sci USA, 86:1173-77, 1989; PCT Patent Application WO 88/10315 etal., 1989 (each incorporated herein by reference).

[0140] In NASBA, the nucleic acids can be prepared for amplification bystandard phenol/chloroform extraction, heat denaturation of a clinicalsample, treatment with lysis buffer, and minispin columns for isolationof DNA and RNA or guanidinium chloride extraction of RNA. Theseamplification techniques involve annealing a primer which has targetspecific sequences. Following polymerization, DNA/RNA hybrids aredigested with RNase H while double stranded DNA molecules are heatdenatured again. In either case the single stranded DNA is made fullydouble stranded by addition of second target specific primer, followedby polymerization. The double-stranded DNA molecules are then multiplytranscribed by a polymerase such as T7 or SP6. In an isothermal cyclicreaction, the RNAs are reverse transcribed into double stranded DNA, andtranscribed once again with a polymerase such as T7 or SP6. Theresulting products, whether truncated or complete, indicate targetspecific sequences.

[0141] viii. Other Amplification Methods

[0142] Other amplification methods, as described in British PatentApplication No. GB 2,202,328, and in PCT Patent Application No.PCT[US89/01025, each incorporated herein by reference, may be used inaccordance with the present disclosure. In the former application,“modified” primers are used in a PCR™-like template and enzyme dependentsynthesis. The primers may be modified by labeling with a capture moiety(e.g., biotin) and/or a detector moiety (e.g., enzyme). In the latterapplication, an excess of labeled probes are added to a sample. In thepresence of the target sequence, the probe binds and is cleavedcatalytically. After cleavage, the target sequence is released intact tobe bound by excess probe. Cleavage of the labeled probe signals thepresence of the target sequence.

[0143] Davey et al., European Patent Application No. 329,822(incorporated herein by reference) disclose a nucleic acid amplificationprocess involving cyclically synthesizing single-stranded RNA (“ssRNA”),ssDNA, and double-stranded DNA (dsDNA), which may be used in accordancewith the present disclosure. The ssRNA is a first template for a firstprimer oligonucleotide, which is elongated by reverse transcriptase(RNA-dependent DNA polymerase). The RNA is then removed from theresulting DNA:RNA duplex by the action of ribonuclease H (RNase H, anRNase specific for RNA in duplex with either DNA or RNA). The resultantssDNA is a second template for a second primer, which also includes thesequences of an RNA polymerase promoter (exemplified by T7 RNApolymerase) 5′ of its homology to the template. This primer is thenextended by DNA polymerase (exemplified by the large “Klenow” fragmentof E.coli DNA polymerase I), resulting in a double-stranded DNAmolecule, having a sequence identical to that of the original RNAbetween the primers and having additionally, at one end, a promotersequence. This promoter sequence can be used by the appropriate RNApolymerase to make many RNA copies of the DNA. These copies can thenreenter the cycle leading to very swift amplification. With properchoice of enzymes, this amplification can be done isothermally withoutadding enzymes at each cycle. Because of the cyclical nature of thisprocess, the starting nucleic acid sequence can be either DNA or RNA.

[0144] Miller et al., PCT Patent Application WO 89/06700 (incorporatedherein by reference), disclose a nucleic acid sequence amplificationscheme based on the hybridization of a promoter/primer sequence to atarget single-stranded DNA followed by transcription of many RNA copiesof the sequence. This scheme is not cyclic, i.e., new templates are notproduced from the resultant RNA transcripts.

[0145] Other suitable amplification methods include “race and “one-sidedPCR™” (Frohman, In: PCR Protocols: A Guide To Methods And Applications,Academic Press, N.Y., 1990, each herein incorporated by reference).Methods based on ligation of two (or more) oligonucleotides in thepresence of nucleic acid having the sequence of the resulting“di-oligonucleotide,” thereby amplifying the di-oligonucleotide, alsomay be used to amplify DNA in accordance with the present disclosure (Wuet al., Genomics 4:560-569, 1989, incorporated herein by reference).

[0146] 3. Restriction Enzymes

[0147] Restriction enzymes recognize specific short DNA sequences fourto eight nucleotides long (see Table 1), and cleave DNA at a site withinthis sequence. In the context of the present disclosure, restrictionenzymes may be used to cleave DNA molecules at sites corresponding tovarious restriction-enzyme recognition sites prior to or subsequent tothe amplification reaction.

[0148] Since the sequence of the recognition site for a variety ofrestriction enzymes is well known in the art (e.g., see Table 1 below),primers can be designed that contain nucleotides corresponding to therecognition sequences. Primer sets can have in addition to therestriction recognition sequence degenerate sequences corresponding todifferent combinations of nucleotide sequences. Table 1 belowexemplifies restriction enzymes and their cleavage sites that may beuseful in the present disclosure. TABLE 1 RESTRICTION ENZYMES EnzymeName Recognition Sequence AatII GACGTC Acc65 I GGTACC Acc I GTMKAC Aci ICCGC Acl I AACGTT Afe I AGCGCT Afl II CTTAAG Afl III ACRYGT Age I ACCGGTAhd I GACNNNNNGTC Alu I AGCT Alw I GGATC AlwN I CAGNNNCTG Apa I GGGCCCApaL I GTGCAC Apo I RAATTY Asc I GGCGCGCC Ase I ATTAAT Ava I CYCGRG AvaII GGWCC Avr II CCTAGG Bae I NACNNNNGTAPyCN BamH I GGATCC Ban I GGYRCCBan II GRGCYC Bbs I GAAGAC Bbv I GCAGC BbvC I CGTCAGC Bcg I CGANNNNNNTGCBciV I GTATCC Bcl I TGATCA Bfa I CTAG Bgl I: GCCNNNNNGGC Bgl II AGATCTBlp I GCTNAGC Bmr I ACTGGG Bpm I CTGGAG BsaA I YACGTR BsaB I GATNNNNATCBsaH I GRCGYG Bsa I GGTCTC BsaJ I CGNNGG BsaW I WCCGGW BseR I GAGGAG BsgI GTGCAG BsiE I CGRYCG BsiHKA I GWGCWC BsiW I CGTACG Bsl I CCNNNNNNNGGBsmA I GTCTC BsmB I CGTCTC BsmF I GGGAC Bsm I GAATGC BsoB I CYCGRGBsp1286 I GDGGHC BspD I ATCGAT BspE I TCCGGA BspH I TCATGA BspM I ACCTGCBsrB I CCGCTC BsrD I GCAATG BsrF I RCCGGY BsrG I TGTACA Bsr I ACTGG BssHII GCGCGC BssK I CCNGG Bst4C I ACNGT BssS I CACGAG BstAP I GCANNNNNTGCBstB I TTCGAA BstE II GGTNACC BstF5 I GGATGNN BstN I CCWGG BstU I CGCGBstX I CCANNNNNNTGG BstY I RGATCY BstZ17 I GTATAC Bsu36 I CCTNAGG Btg ICCPuPyGG Btr I CACGTG Cac8 I GGNNGC Cla I ATCGAT Dde I CTNAG Dpn I GATCDpn II GATC Dra I TTTAAA Dra III CACNNNGTG Drd I GAGNNNNNNGTC Eae IYGGCCR Eag I CGGCCG Ear I CTCTTC Eci I GGCGGA EcoN I CCTNNNNNAGG EcoO109I RGGNCCY EcoR I GAATTC EcoR V GATATC Fau I CCCGCNNNN Fnu4H I GCNGC FokI GGATG Fse I GGCCGGGC Fsp I TGCGCA Hae II RGCGCY Hae III GGCC Hga IGACGC Hha I GCGC Hinc II GTYRAC Hind III AAGCTT Hinf I GANTC HinPl IGCGC Hpa I GTTAAC Hpa II CCGG Hph I GGTGA Kas I GGCGCC Kpn I GGTACC MboI GATC Mbo II GAAGA Mfe I CAATTG Mlu I ACGCGT Mly I GAGTGNNNNN Mnl ICCTC Msc I TGGCCA Mse I TTAA Msl I CAYNNNNRTG MspAl I CMGCKG Msp I CCGGMwo I GCNNNNNNNGC Nae I GCCGGC Nar I GGCGCC Nci I CCSGG Nco I GCATGG NdeI CATATG NgoMI V GCCGGC Nhe I GCTAGC Nla III CATG Nla IV GGNNCC Not IGCGGCCGC Nru I TCGCGA Nsi I ATGCAT Nsp I RCATGY Pac I TTAATTAA PaeR7 ICTCGAG Pci I ACATGT PflF I GACNNNGTC PflM I CCANNNNNTGG Ple I GAGTC PmeI GTTTAAAC Pml I CACGTG PpuM I RGGWCCY PshA I GACNNNNGTC Psi I TTATAAPspG I CCWGG PspOM I GGGCCC Pst I CTGCAG Pvu I GGATGG Pvu II CAGCTG RsaI GTAC Rsr II GGGWCCG Sac I GAGCTC Sac II CCGCGG Sal I GTCGAC Sap IGCTCTTG Sau3A I GATC Sau96 I GGNCC Sbf I CCTGCAGG Sca I AGTACT ScrF ICCNGG SexA I ACCWGGT SfaN I GCATC Sfc I CTRYAG Sfi I GGCCNNNNNGGCC Sfo IGGCGCC SgrA I CRCCGGYG Sma I CCCGGG Sml I CTYRAG SnaB I TACGTA Spe IACTAGT Sph I GCATGC Ssp I AATATT Stu I AGGCCT Sty I CCWWGG Swa IATTTAAAT Taq I TCGA Tfi I GAWTC Tli I CTCGAG Tse I GCWGC Tsp45 I GTSACTsp5O9 I AATT TspR I CAGTG Tthlll I GACNNNGTC Xba I TCTAGA Xcm ICCANNNNNNNNNTGG Xho I CTCGAG Xma I CCCGGG Xmn I GAANNNNTTC

[0149] 4. Other Enzymes

[0150] A polymerase is an enzyme that catalyses the synthesis of nucleicacids on preexisting nucleic acid templates, assembling RNA fromribonucleotides or DNA from deoxyribonucleotides. Polymerasesspecifically contemplated in the context of the present disclosure maybe naturally isolated, modified, or synthetic. While it is generallycontemplated that the polymerase employed will be thermostable,non-thermostable polymerases may also be employed in the context of thepresent disclosure. Tables 2 and 3 set forth exemplary polymerases andnucleic acid modifying enzymes that may be used in the context of thedisclosure. TABLE 2 POLYMERASES Thermostable DNA Polymerases: OmniBase™Sequencing Enzyme Pfu DNA Polymerase Taq DNA Polymerase Taq DNAPolymerase, Sequencing Grade TaqBead™ Hot Start Polymerase AmpliTaq GoldVent DNA Polymerase Tub DNA Polymerase TaqPlus DNA Polymerase Tfl DNAPolymerase Tli DNA Polymerase Tth DNA Polymerase DNA Polymerases: DNAPolymerase I, Klenow Fragment, Exonuclease Minus DNA Polymerase I DNAPolymerase I Large (Klenow) Fragment Terminal DeoxynucleotidylTransferase T7 DNA Polymerase T4 DNA Polymerase REVERSE TRANSCRIPTASESAMV Reverse Transcriptase M-MLV Reverse Transcriptase

[0151] TABLE 3 DNA/RNA MODIFYING ENZYMES Ligases: T4 DNA Ligase Kinases:T4 Polynucleotide Kinase

[0152] 5. Labels

[0153] Recognition moieties incorporated into primers, incorporated intothe amplified product during amplification, or attached to probes areuseful in identification of the amplified molecules. A number ofdifferent labels may be used for this purpose such as, for example:fluorophores, chromophores, radio-isotopes, enzymatic tags, antibodies,chemiluminescence, electroluminescence, affinity labels, etc. One ofskill in the art will recognize that these and other fluorophores notmentioned herein can also be used with success in this disclosure.

[0154] Examples of affinity labels include but are not limited to thefollowing: an antibody, an antibody fragment, a receptor protein, ahormone, biotin, DNP, or any polypeptide/protein molecule that binds toan affinity label and may be used for separation of the amplified gene.

[0155] Examples of enzyme tags include enzymes such as urease, alkalinephosphatase, or peroxidase. Additionally, colorimetric indicatorsubstrates can be employed to provide a detection means visible to thehuman eye or spectrophotometrically, to identify specific hybridizationwith complementary nucleic acid-containing samples. All these examplesare generally known in the art and the skilled artisan will recognizethat the present disclosure is not limited to the examples describedabove.

[0156] The following fluorophores are specifically contemplated to beuseful in the present disclosure: Alexa 350, Alexa 430, AMCA, BODIPY630/650, BODIPY 650/665, BODIPY-FL, BODIPY-R6G, BODIPY-TMR, BODIPY-TRX,Cascade Blue, Cy2, Cy3, CyS, 6-FAM, Fluorescein, HEX, 6-JOE, OregonGreen 488, Oregon Green 500, Oregon Green 514, Pacific Blue, REG,Rhodamine Green, Rhodamine Red, ROX, TAMRA, TET, Tetramethylrhodamine,and Texas Red.

[0157] 6. Separation and Quantitation Methods

[0158] Following amplification, it may be desirable to separate theamplification products of several different lengths from each other,from the template, and from excess primers for the purpose of analysisor more specifically for determining whether specific amplification hasoccurred.

[0159] i Gel electrophoresis

[0160] In one embodiment, amplification products are separated byagarose, agarose-acrylamide or polyacrylamide gel electrophoresis usingstandard methods (Sambrook et al., “Molecular Cloning,” A LaboratoryManual, 2d Ed., Cold Spring Harbor Laboratory Press, New York,13.7-13.9:1989). Gel electrophoresis techniques are well known in theart.

[0161] ii. Chromatographic Techniques

[0162] Alternatively, chromatographic techniques may be employed toeffect separation. There are many kinds of chromatography which may beused in the present disclosure: adsorption, partition, ion-exchange, andmolecular sieve, as well as many specialized techniques for using themincluding column, paper, thin-layer and gas chromatography (Freifelder,Physical Biochemstry Applications to Biochemistry and Molecular Biology,2nd ed. Wm. Freeman and Co., New York, N.Y., 1982). Yet anotheralternative is to capture nucleic acid products labeled with, forexample, biotin or antigen with beads bearing avidin or antibody,respectively.

[0163] iii. Microfluidic Techniques

[0164] Microfluidic techniques include separation on a platform such asmicrocapillaries, including by way of example those designed by ACLARABioSciences Inc., or the LabChip™ by Caliper Technologies Inc. Thesemicrofluidic platforms require only nanoliter volumes of sample, incontrast to the microliter volumes required by other separationtechnologies. Miniaturizing some of the processes involved in geneticanalysis has been achieved using microfluidic devices. For example,published PCT Application No. WO 94/05414, to Northrup and White,incorporated herein by reference, reports an integrated micro-PCR™apparatus for collection and amplification of nucleic acids from aspecimen. U.S. Pat. Nos. 5,304,487, 5,296,375, and 5,856,174 describeapparatus and methods incorporating the various processing andanalytical operations involved in nucleic acid analysis and areincorporated herein by reference.

[0165] iv. Capillary Electrophoresis

[0166] In some embodiments, it may be desirable to provide anadditional, or alternative means for analyzing the amplified DNA. Inthese embodiments, microcapillary arrays are contemplated to be used forthe analysis. Microcapillary array electrophoresis generally involvesthe use of a thin capillary or channel that may or may not be filledwith a particular separation medium. Electrophoresis of a sample throughthe capillary provides a size based separation profile for the sample.Microcapillary array electrophoresis generally provides a rapid methodfor size-based sequencing, PCR™ product analysis, and restrictionfragment sizing. The high surface to volume ratio of these capillariesallows for the application of higher electric fields across thecapillary without substantial thermal variation across the capillary,consequently allowing for more rapid separations. Furthermore, whencombined with confocal imaging methods, these methods providesensitivity in the range of attomoles, which is comparable to thesensitivity of radioactive sequencing methods. Microfabrication ofmicrofluidic devices including microcapillary electrophoretic deviceshas been discussed in detail in, for example, Jacobson et al., AnalChem, 66:1107-1113, 1994; Effenhauser et al., Anal Chem, 66:2949-2953,1994; Harrison et al., Science, 261:895-897, 1993; Effenhauser et al.,Anal Chem, 65:2637-2642, 1993; Manz et al., J. Chromatogr 593:253-258,1992; and U.S. Pat. No. 5,904,824, incorporated herein by reference.Typically, these methods comprise photolithographic etching of micronscale channels on a silica, silicon, or other crystalline substrate orchip, and can be readily adapted for use in the present disclosure.

[0167] Tsuda et al. (Anal Chem, 62:2149-2152, 1990) describesrectangular capillaries, an alternative to the cylindrical capillaryglass tubes. Some advantages of these systems are their efficient heatdissipation due to the large height-to-width ratio and, hence, theirhigh surface-to-volume ratio and their high detection sensitivity foroptical on-column detection modes. These flat separation channels havethe ability to perform two-dimensional separations, with one force beingapplied across the separation channel, and with the sample zonesdetected by the use of a multi-channel array detector.

[0168] In many capillary electrophoresis methods, the capillaries, e.g.,fused silica capillaries or channels etched, machined, or molded intoplanar substrates, are filled with an appropriate separation/sievingmatrix. Typically, a variety of sieving matrices known in the art may beused in the microcapillary arrays. Examples of such matrices include,e.g., hydroxyethyl cellulose, polyacrylamide, agarose, and the like.Generally, the specific gel matrix, running buffers, and runningconditions are selected to maximize the separation characteristics ofthe particular application, e.g., the size of the nucleic acidfragments, the required resolution, and the presence of native orundenatured nucleic acid molecules. For example, running buffers mayinclude denaturants, chaotropic agents such as urea to denature nucleicacids in the sample.

[0169] v. Mass Spectroscopy

[0170] Mass spectrometry provides a means of “weighing” individualmolecules by ionizing the molecules in vacuo and making them “fly” byvolatilization. Under the influence of combinations of electric andmagnetic fields, the ions follow trajectories depending on theirindividual mass (m) and charge (z). For low molecular weight molecules,mass spectrometry has been part of the routine physical-organicrepertoire for analysis and characterization of organic molecules by thedetermination of the mass of the parent molecular ion. In addition, byarranging collisions of this parent molecular ion with other particles(e.g., argon atoms), the molecular ion is fragmented forming secondaryions by the so-called collision induced dissociation (CID). Thefragmentation pattern/pathway very often allows the derivation ofdetailed structural information. Other applications of massspectrometric methods in the art are summarized in Methods inEnzymology, Vol. 193: “Mass Spectrometry” (J. A. McCloskey, editor),1990, Academic Press, New York.

[0171] Due to the apparent analytical advantages of mass spectrometry inproviding high detection sensitivity, accuracy of mass measurements,detailed structural information by CID in conjunction with an MS/MSconfiguration and speed, as well as on-line data transfer to a computer,there has been considerable interest in the use of mass spectrometry forthe structural analysis of nucleic acids. Reviews summarizing this fieldinclude (Schram, Methods Biochem Anal, 34:203-287, 1990) and (Crain,Mass Spectrometry Reviews, 9:505-554, 1990), here incorporated herein byreference. The biggest hurdle to applying mass spectrometry to nucleicacids is the difficulty of volatilizing these very polar biopolymers.Therefore, “sequencing” had been limited to low molecular weightsynthetic oligonucleotides by determining the mass of the parentmolecular ion and through this, confirming the already known sequence,or alternatively, confirming the known sequence through the generationof secondary ions (fragment ions) via CID in an MS/MS configurationutilizing, in particular, for the ionization and volatilization, themethod of fast atomic bombardment (FAB mass spectrometry) or plasmadesorption (PD mass spectrometry). As an example, the application of FABto the analysis of protected dimeric blocks for chemical synthesis ofoligodeoxynucleotides has been described (Koster et al., BiomedicalEnvironmental Mass Spectrometry 14:111-116, 1987).

[0172] Two ionization/desorption techniques are electrospray/ionspray(ES) and matrix-assisted laser desorption/ionization (MALDI). ES massspectrometry was introduced by Fenn et al., J. Phys. Chem. 88;4451-59,1984; PCT Application No. WO 90/14148 and its applications aresummarized in review articles, for example, Smith et al., Anal Chem62:882-89, 1990, and Ardrey, Electrospray Mass Spectrometry,Spectroscopy Europe, 4:10-18, 1992. As a mass analyzer, a quadrupole ismost frequently used. The determination of molecular weights infemtomole amounts of sample is very accurate due to the presence ofmultiple ion peaks that can be used for the mass calculation.

[0173] MALDI mass spectrometry, in contrast, can be particularlyattractive when a time-of-flight (TOF) configuration is used as a massanalyzer. The MALDI-TOF mass spectrometry was introduced by (Hillenkampet al., Biological Mass Spectrometry eds. Burlingame and McCloskey,Elsevier Science Publishers, Amsterdam, pp. 49-60, 1990). Since, in mostcases, no multiple molecular ion peaks are produced with this technique,the mass spectra, in principle, look simpler compared to ES massspectrometry. DNA molecules up to a molecular weight of 410,000 daltonscould be desorbed and volatilized (Williams et al., Science,246:1585-87, 1989). More recently, the use of infrared lasers (IR) inthis technique (as opposed to UV-lasers) has been shown to provide massspectra of larger nucleic acids such as synthetic DNA, restrictionenzyme fragments of plasmid DNA, and RNA transcripts up to a size of2180 nucleotides (Berkenkamp et al., Science, 281:260-2, 1998).Berkenkamp also describes how DNA and RNA samples can be analyzed bylimited sample purification using MALDI-TOF IR.

[0174] In Japanese Patent No. 59-131909, an instrument is described thatdetects nucleic acid fragments separated either by electrophoresis,liquid chromatography or high speed gel filtration. Mass spectrometricdetection is achieved by incorporating into the nucleic acids atoms thatnormally do not occur in DNA such as S, Br, I or Ag, Au, Pt, Os, Hg.

[0175] vii. Energy Transfer

[0176] Labeling hybridization oligonucleotide probes with fluorescentlabels is a well known technique in the art and is a sensitive,nonradioactive method for facilitating detection of probe hybridization.More recently developed detection methods employ the process offluorescence energy transfer (FET) rather than direct detection offluorescence intensity for detection of probe hybridization. FET occursbetween a donor fluorophore and an acceptor dye (which may or may not bea fluorophore) when the absorption spectrum of one (the acceptor)overlaps the emission spectrum of the other (the donor) and the two dyesare in close proximity. Dyes with these properties are referred to asdonor/acceptor dye pairs or energy transfer dye pairs. The excited-stateenergy of the donor fluorophore is transferred by a resonancedipole-induced dipole interaction to the neighboring acceptor. Thisresults in quenching of donor fluorescence. In some cases, if theacceptor is also a fluorophore, the intensity of its fluorescence may beenhanced. The efficiency of energy transfer is highly dependent on thedistance between the donor and acceptor, and equations predicting theserelationships have been developed by Forster, Ann Phys 2:55-75, 1948.The distance between donor and acceptor dyes at which energy transferefficiency is 50% is referred to as the Forster distance (Ro). Othermechanisms of fluorescence quenching are also known in the artincluding, for example, charge transfer and collisional quenching.

[0177] Energy transfer and other mechanisms that rely on the interactionof two dyes in close proximity to produce quenching are an attractivemeans for detecting or identifying nucleotide sequences, as such assaysmay be conducted in homogeneous formats. Homogeneous assay formatsdiffer from conventional probe hybridization assays that rely on thedetection of the fluorescence of a single fluorophore label becauseheterogeneous assays generally require additional steps to separatehybridized label from free label. Several formats for FET hybridizationassays are reviewed in Nonisotopic DNA Probe Techniques (Academic Press,Inc., pgs. 311-352, 1992).

[0178] Homogeneous methods employing energy transfer or other mechanismsof fluorescence quenching for detection of nucleic acid amplificationhave also been described. Higuchi et al. (Biotechnology 10:413-417,1992), discloses methods for detecting DNA. amplification in real-timeby monitoring increased fluorescence of ethidium bromide as it binds todouble-stranded DNA. The sensitivity of this method is limited becausebinding of the ethidium bromide is not target specific and backgroundamplification products are also detected. Lee et al. (Nucleic Acids Res21:3761-3766, 1993), discloses a real-time detection method in which adoubly-labeled detector probe is cleaved in a targetamplification-specific manner during PCR™. The detector probe ishybridized downstream of the amplification primer so that the 5′-3′exonuclease activity of Taq polymerase digests the detector probe,separating two fluorescent dyes, which then form an energy transferpair. Fluorescence intensity increases as the probe is cleaved.Published PCT application WO 96/21144 discloses continuous fluorometricassays in which enzyme-mediated cleavage of nucleic acids results inincreased fluorescence. Fluorescence energy transfer is suggested foruse, but only in the context of a method employing a single fluorescentlabel that is quenched by hybridization to the target.

[0179] Signal primers or detector probes that hybridize to the targetsequence downstream of the hybridization site of the amplificationprimers have been described for use in detection of nucleic acidamplification (U.S. Pat. No. 5,547,861). The signal primer is extendedby the polymerase in a manner similar to extension of the amplificationprimers. Extension of the amplification primer displaces the extensionproduct of the signal primer in a target amplification-dependent manner,producing a double-stranded secondary amplification product that may bedetected as an indication of target amplification. The secondaryamplification products generated from signal primers may be detected bymeans of a variety of labels and reporter groups, restriction sites inthe signal primer that are cleaved to produce fragments of acharacteristic size, capture groups, and structural features such astriple helices and recognition sites for double-stranded DNA bindingproteins.

[0180] Many donor/acceptor dye pairs are known in the art and may beused in the present disclosure. These include but are not limited to:fluorescein isothiocyanate (FITC)/tetramethylrhodamine isothiocyanate(TALIC), FITC/Texas Red™ Molecular Probes, FITC/N-hydroxysuccmimidyl1-pyrenebutyrate (PYB), FITC/eosin isothiocyanate (EITC),N-hydroxysuccinimidyl 1-pyrenesulfonate (PYS)/FITC, FITC/Rhodamine X,FITC/tetramethylrhodamine (TAMRA), and others. The selection of aparticular donor/acceptor fluorophore pair is not critical. For energytransfer quenching mechanisms it is only necessary that the emissionwavelengths of the donor fluorophore overlap the excitation wavelengthsof the acceptor, i.e., there must be sufficient spectral overlap betweenthe two dyes to allow efficient energy transfer, charge transfer, orfluorescence quenching. P-(dimethyl aminophenylazo)benzoic acid (DABCYL)is a non-fluorescent acceptor dye which effectively quenchesfluorescence from an adjacent fluorophore, e.g., fluorescein or5-(2′-aminoethyl)aminonaphthalene (EDANS). Any dye pairs that producefluorescence quenching in the detector nucleic acids are suitable foruse in the methods of the disclosure, regardless of the mechanism-bywhich quenching occurs. Terminal and internal labeling methods are bothknown in the art and may be routinely used to link the donor andacceptor dyes at their respective sites in the detector nucleic acid.

[0181] viii. Microarrays and Chip Technologies

[0182] Specifically contemplated in the present disclosure is the use oranalysis of amplified products by microarrays and/or chip-based DNAtechnologies such as those described by (Hacia et al., Nature Genet,14:441-449, 1996) and (Shoemaker et al., Nature Genetics, 14:450-456,1996). These techniques involve quantitative methods for analyzing largenumbers of genes rapidly and accurately. By tagging genes witholigonucleotides or using fixed probe arrays, chip technology can beemployed to segregate target molecules as high density arrays and screenthese molecules on the basis of hybridization (Pease et al., Proc NatlAcad Sci USA, 91:5022-5026, 1994; Fodor et al, Nature, 364:555-556,1993).

[0183] ix. OIA.

[0184] Also contemplated is the use of BioStar's OIA technology toquantitate amplified products. OIA uses the mirror-like surface of asilicon wafer as a substrate. A thin film optical coating and captureantibody is attached to the silicon wafer. White light reflected throughthe coating appears as a golden background color. This color does notchange until the thickness of the optical molecular thin film ischanged.

[0185] When a positive sample is applied to the wafer, binding occursbetween the ligand and the antibody. When substrate is added to completethe mass enhancement, a corresponding change in color from gold topurple/blue results from the increased thickness in the molecular thinfilm. The technique is described in U.S. Pat. No. 5,541,057, hereinincorporated by reference.

[0186] x. Real Time PCR

[0187] Amplified RNA or DNA may be quantitated using the Real-Time PCRtechnique (Higuchi et al., Biotechnology 10:413-417, 1992). Bydetermining the concentration of the amplified products that havecompleted the same number of cycles and are in their linear ranges, itis possible to determine the relative concentrations of the specifictarget sequence in the original DNA mixture. For example, if the DNAmixtures are cDNAs synthesized from RNAs isolated from different tissuesor cells, the relative abundance of the specific mRNA from which thetarget sequence was derived can be determined for the respective tissuesor cells. This direct proportionality between the concentration of theamplification products and the relative mRNA abundance is only true inthe linear range of the amplification reaction.

[0188] The final concentration of the target DNA in the plateau portionof the curve is determined by the availability of reagents in thereaction mixture and is independent of the original concentration oftarget DNA. Therefore, the first condition that must be met before therelative abundance of a RNA or DNA species can be determined byReal-Time PCR for a collection of RNA or DNA populations is that theconcentrations of the amplified products must be sampled when thereaction products are in the linear portion of their curves. The secondcondition that must be met for an RT-PCR experiment to successfullydetermine the relative abundance of a particular mRNA species is thatrelative concentrations of the amplifiable cDNAs must be normalized tosome independent standard. The goal of a Real-Time PCR experiment is todetermine the abundance of a particular RNA or DNA species relative tothe average abundance of all RNA or DNA species in the sample.

[0189] xi. Luminex

[0190] The Luminex technology allows the quantitation of nucleic acidproducts immobilized on color coded microspheres. The magnitude of thebiomolecular reaction is measured using a second molecule called areporter. The reporter molecule signals the extent of the reaction byattaching to the molecules on the microspheres. As both the microspheresand the reporter molecules are color coded, digital signal processingallows the translation of signals into real-time, quantitative data foreach reaction. The standard technique is described in U.S. Pat. Nos.5,736,303 and 6,057,107, herein incorporated by reference.

[0191] 8. Identification Methods

[0192] Amplification products must be visualized in order to confirmamplification of the target-gene(s) sequences. One typical visualizationmethod involves staining of a gel with a flourescent dye, such asethidium bromide or Vistra Green, and visualization under UV light.Alternatively, if the amplification products are integrally labeled withradio- or fluorometrically-labeled nucleotides, the amplificationproducts can be exposed to x-ray film or visualized under theappropriate stimulating spectra following separation.

[0193] In one embodiment, visualization is achieved indirectly, using anucleic acid probe. Following separation of amplification products, alabeled, nucleic acid probe is brought into contact with the amplifiedproducts. The probe preferably is conjugated to a chromophore but may beradiolabeled. In another embodiment, the probe is conjugated to abinding partner, such as an antibody or biotin, where the other memberof the binding pair carries a detectable moiety. In other embodiments,the probe incorporates a fluorescent dye or label. In yet otherembodiments, the probe has a mass label that can be used to detect themolecule amplified. Other embodiments also contemplate the use ofTaqman™ and Molecular Beacon™ probes. In still other embodiments,solid-phase capture methods combined with a standard probe may be used.

[0194] The type of label incorporated in DNA amplification products isdictated by the method used for analysis. When using capillaryelectrophoresis, microfluidic electrophoresis, HPLC, or LC separations,either incorporated or intercalated fluorescent dyes are used to labeland detect the amplification products. Samples are detected dynamically,in that fluorescence is quantitated as a labeled species moves past thedetector. If any electrophoretic method, HPLC, or LC is used forseparation, products can be detected by absorption of UV light, aproperty inherent to DNA and therefore not requiring addition of alabel. If polyacrylamide gel or slab gel electrophoresis is used,primers for the amplification reactions can be labeled with afluorophore, a chromophore or a radioisotope, or by associated enzymaticreaction. Enzymatic detection involves binding an enzyme to a primer,e.g., via a biotin:avidin interaction, following separation of theamplification products on a gel, then detection by chemical reaction,such as chemiluminescence generated with luminol. A fluorescent signalcan be monitored dynamically. Detection with a radioisotope or enzymaticreaction requires an initial separation by gel electrophoresis, followedby transfer of DNA molecules to a solid support (blot) prior toanalysis. Ifblots are made, they can be analyzed more than once byprobing, stripping the blot, and then reprobing. If amplificationproducts are separated using a mass spectrometer no label is requiredbecause nucleic acids are detected directly.

[0195] A number of the above separation platforms can be coupled toachieve separations based on two different properties. For example, someof the PCR™ primers can be coupled with a moiety that allows affinitycapture, while some primers remain unmodified. Modifications can includea sugar (for binding to a lectin column), a hydrophobic group (forbinding to a reverse-phase column), biotin (for binding to astreptavidin column), or an antigen (for binding to an antibody column).Samples are run through an affinity chromatography column. Theflow-through fraction is collected, and the bound fraction eluted (bychemical cleavage, salt elution, etc.). Each sample is then furtherfractionated based on a property, such as mass, to identify individualcomponents.

[0196] 10. Kits

[0197] The materials and reagents required for the disclosedamplification method may be assembled together in a kit. The kits of thepresent disclosure generally will include at least the enzymes andnucleotides necessary to carry out the claimed method along with primersets. In a preferred embodiment, the kit will also contain directionsfor amplifying DNA from DNA samples.

[0198] The kits of the present disclosure also will generally includeone or more preselected primer sets and/or probes that may be eitherspecific or non-specific for genes to be amplified. Preferably, the kitswill include, in a suitable container means, one or more nucleic acidprobes and/or primer sets and means for detecting nucleic acids. Incertain embodiments, such as in kits for use in amplification reactions,the means for detecting the nucleic acids may be a label, such as afluorophore, a radiolabel, an enzyme tag, etc., that is linked to thenucleic acid primer or the nucleotides themselves. It is envisioned thatkits may contain pairs of primer sets for each DNA amplification step ofthe present disclosure. It is also envisioned that kits may containprecipitation solutions to process DNA samples stored on solid mediumsaccording to the precipitation method of the present disclosure.

[0199] Preferred kits are those suitable for use in amplifying wholegenomic DNA. In a preferred kit, a first primer will preferably beprovided that has a random sequence of nucleotides at its 3′ end and ageneric 5′ of the random sequence, which hybridizes randomly to DNA. Thekit will also preferably include a second primer with a generic sequencethat is the same as the generic sequence of the first primer. Forexample, kits may be used to amplify all genes and chromosomal regions,unknown and/or known from an organisms whole genomic or chromosomal DNA.Also included in the kits may be enzymes suitable for amplifying nucleicacids, including various polymerases (RT, Taq, etc.), deoxynucleotidesand buffers to provide the necessary single reaction mixture foramplification.

[0200] The kits of the present disclosure, may also contain primers withone or more of a variety of other moieties as described above.

[0201] In each case, the kits will preferably have distinct containersfor each individual reagent and enzyme, as well as for each probe orprimer pair. Each biological agent will generally be suitably aliquotedin their respective containers. The container means of the kits willgenerally include at least one vial or test tube. Flasks, bottles, andother container means into which the reagents are placed and aliquotedare also possible. The individual containers of the kit will preferablybe maintained in close confinement for commercial sale. Suitable largercontainers may include injection or blow-molded plastic containers intowhich the desired vials are retained. Instructions are preferablyprovided with the kit.

[0202] The following examples are included to demonstrate preferredembodiments of the present disclosure. It should be appreciated by thoseof skill in the art that the techniques disclosed in the examples whichfollow represent techniques discovered by the inventor to function wellin the practice of the invention, and thus can be considered toconstitute preferred modes for its practice. However, those of skill inthe art should, in light of the present disclosure, appreciate that manychanges can be made in the specific embodiments that are disclosed andstill obtain a like or similar result without departing from the spiritand scope of the invention.

EXAMPLE 1

[0203] The efficiency of PCR™ amplification of DNA samples stored on FTApaper processed using the presently disclosed precipitation method andthe commercially produced FTA Purification Reagent (manufactured byWhatman) protocol was compared. First, four bloodstain DNA samplesstored on FTA paper were processed using the disclosed precipitationmethod according to the following protocol: A small circle (1-3 mm) inthe FTA paper sample was excised by the commercial Harris Micro-Punchmanufactured by Shunderson Communication, Ottawa, Ontario, Canada, andwashed with distilled water. The circle was transferred to a 96-wellplate and soaked in 200 μl of DD H₂O for 20 minutes. The water waschanged and the circle was soaked in water again for 5 minutes. Thewater was next replaced with 200 μl of 0.3 M NaOAc/Ethanol (50/50 v/v)solution and the paper was soaked for 5 minutes to fix the genomic DNAon the paper. The solution was removed and the paper was washed in 200μl of 80% ethanol for 5 minutes to remove salt and to acceleratedehydration. The ethanol was removed and the paper was dried at roomtemperature for 15 minutes. The ethanol wash reduced the dehydrationtime of the FTA paper sample by at least 50%. The dehydrated paper wasthen used directly as the DNA for PCR amplification.

[0204] Second, the same four bloodstain DNA samples stored on FTA paperwere processed according to the commercial FTA Purification Reagentmanufacturer's protocol. Briefly, for each sample a small circle (1-3mm) in the FTA paper sample was excised by the Harris Micro-Punch. Thecircle was transferred to a 96-well plate and soaked in 200 μl of FTAPurification Reagent for 5 minutes. The FTA reagent was changed and thewash was repeated 2 times. After the FTA Purification Reagent had beenremoved for the third time, 200 μl of TE buffer (10 mM Tris-HCl pH 8.0and 0.1 mM EDTA) was added to the paper. The FTA paper was soaked in TEfor 5 minutes, and then the TE solution was removed and the paper wasair-dried for 1 hour. The dehydrated paper was then used directly forPCR amplification.

[0205] Both sets of dehydrated paper samples were amplified using thefollowing conditions. The reaction mixture for each PCR contained theDNA-paper sample, 10 mM Tris HCl (pH 8.3), 5 mM MgCl₂, 50 mM KCl, 0.001%gelatin, 300 μM dNTP (dATP, dGTP, dCTP, and dTTP), 300 nM of the forwardprimer having the sequence 5′-CCTTTTCCTCTAGCATCAAGTTA-3′ (SEQ ID NO:13), 300 μM of the reverse primer having the sequence5′-CAGACTGTGTGCTTCCTACAG-3′ (SEQ ID NO: 14), and 1.25 unit Taq DNApolymerase, for a total volume of 50 μM. The thermocycling program forthe reaction mixtures was 95° C. for 2 minutes; 15 “touchdown” cycles of95° C. for 30 seconds, 66−51° C. for 30 seconds, and 72° C. for 30seconds; and 35 cycles of 95° C. for 30 seconds 50° C. for 30 seconds,and 72° C. for 30 seconds. The PCR products were subjected toelectrophoresis on a 2.0% agarose gel without purification.

[0206]FIG. 2 shows the results of direct PCR amplification of DNAsamples stored on FTA paper processed using the disclosed precipitationmethod as compared to the FTA Purification Reagent protocol. FIG. 2.clearly demonstrates that the disclosed precipitation method greatlyreduces the variation of PCR amplification efficiency found when thecommercial FTA Purification Reagent is used to process DNA samples. Thepresently disclosed precipitation method not only offers a simpler andfaster method for processing DNA samples stored on FTA paper, it alsoreduces the cost of processing the samples and greatly optimizessubsequent PCR amplification and genetic analysis of the DNA samples.

EXAMPLE 2

[0207] The method of amplifying whole genomic DNA of the presentdisclosure was used to amplify genomic DNA from bovine bloodstainsamples stored on FTA paper. This method combines DNA extraction andamplification in a single operation by allowing genomic DNA in a bovinebloodstain sample to be amplified in a single reaction mixture using asingle thermocycling reaction. Therefore, this method greatly reducesthe risk of sample contamination and facilitates high-throughputscreening. Additionally, 96-well or 384-well plates can be utilized foramplification of genomic DNA stored on FTA paper using the presentlydisclosed methods, which greatly facilitates a high-throughputoperation. The utility and efficiency of the presently disclosed methodof DNA amplification was tested by comparing PCR amplification of aknown bovine SNP locus using DNA amplified by the disclosed method andDNA bound directly to FTA paper. In both experiments, the DNA samplesstored on FTA paper were processed using the disclosed precipitationmethod as described in Example 1. Therefore, this example is designed tospecifically test the efficacy of the presently disclosed method of DNAamplification for genetic analysis.

[0208] Bloodstain samples were collected and stored on FTA paper for 13individual bovine animals. The FTA paper samples were processed usingthe disclosed precipitation method, and genomic DNA was amplified fromone set of samples using the disclosed method of DNA amplification. Eachdehydrated paper sample was amplified using the following conditions.First, the DNA sample was placed in an amplification reaction mixturethat contained 10 mM Tris HCl (pH 8.3), 5 mM MgCl₂, 50 mM KCl, 0.001%gelatin, 300 μM dNTP (dATP, dGTP, dCTP, and dTTP), 300 nM of the firstprimer having the sequence of SEQ ID NO: 1, 300 nM of the second primerhaving the sequence of SEQ ID NO: 2, and 1.25 unit Taq DNA polymerase,for a total volume of about 50 μl. The entire reaction mixture washeated to 95° C. for 5 minutes to denature the sample.

[0209] Next, during the first set of reactions of DNA amplification, thereaction mixture was heated to a temperature of 95° C. for 1 minute, andcooled to a temperature of 42° C. for 5 minutes. These steps allowed thefirst primer to anneal with the denatured sample DNA and the Taq DNApolymerase to synthesize the complementary strand of DNA from the 3′ endof the first primer. The denaturation, annealing, and extension stepswere repeated again by heating the reaction mixture for 1 minute at 95°C. and then cooling the mixture to 42° C. for 5 minutes.

[0210] The second set of reactions of DNA amplification involvedsubsequently heating the reaction mixture to a temperature of 95° C. for15 seconds, cooling the mixture to a temperature of 65° C. to allow thesecond primer to anneal to the single-stranded DNA products, and raisingthe mixture to a temperature of 68° C., thereby allowing the Taq DNApolymerase to synthesize the complementary strand of DNA from the 3′ endof the second primer. These steps of denaturation, annealing, andextension were repeated 39 times for a total of 40 cycles.

[0211] The set of dehydrated DNA samples processed using the disclosedprecipitation method only, and the set of DNA samples processed usingthe disclosed precipitation method, as well as amplified using thedisclosed DNA amplification method, were next subjected to PCRamplification using the following conditions. The reaction mixture foreach PCR contained either the dehydrated DNA-paper sample or 20 ng ofamplified genomic DNA, 10 mM Tris HCl (pH 8.3), 5 MM MgCl₂, 50 mM KCl,0.001% gelatin, 300 μM dNTP (dATP, dGTP, dCTP, and dTTP), 300 nM of theforward primer having the sequence 5′-CCAGCAGTTCTGAATGAAAGT-3′ (SEQ IDNO: 15), 300 nM of the reverse primer having the sequence5′-ACACACAGAGGCCGTGTA-3′ (SEQ ID NO: 16), and 1.25 unit Taq DNApolymerase, for a total volume of 50 μl. The thermocycling program forthe reaction mixtures was 95° C. for 2 minutes; 15 “touchdown” cycles of95° C. for 30 seconds, 66−51° C. for 30 seconds, and 72° C. for 30seconds; and 35 cycles of 95° C. for 30 seconds, 50° C. for 30 seconds,and 72° C. for 30 seconds.

[0212]FIG. 3. shows the products of direct PCR of the known bovine SNPlocus using DNA samples processed according to the disclosedprecipitation method (upper panel), and the identical DNA samplesprocessed according to the disclosed precipitation and DNA amplificationmethod (lower panel). The PCR products are approximately 200 bp inlength, which is the same as that calculated from the known DNAsequence. The visual image of the agarose gel indicates that the methodfor amplifying DNA of the present disclosure generates DNA that can bereadily genotyped using PCR. Additionally, the DNA amplification methodgenerates significantly greater amounts of genomic DNA than can bedirectly isolated from FTA paper. Increasing the amount of availablegenomic DNA by DNA amplification for genotyping will allow for moreextensive analysis of an organism's genotype.

EXAMPLE 3

[0213] To compare the efficiency of the presently disclosed method ofDNA amplification, DNA samples stored on FTA paper were first processedusing the presently disclosed precipitation method or the commercial FTAPurification Reagent protocol, and then amplified according to thedisclosed DNA amplification method. Two sets of punches from sixdifferent bloodstains stored on FTA paper were first treated usingeither the disclosed precipitation method or the FTA PurificationReagent protocol as outlined in Example 1. Next, the two sets of DNAsamples were amplified according to the disclosed DNA amplificationmethod, as outlined in Example 2.

[0214]FIG. 4. demonstrates the results of genomic DNA amplificationusing the disclosed method of DNA amplification. The figure compares theefficiency of the disclosed DNA amplification method when the DNA sampleis processed using the FTA Purification Reagent protocol (lanes 2-7)versus the disclosed precipitation method (lanes 8-13). FIG. 4. clearlydemonstrates that the presently disclosed DNA amplification methodgenerates much greater quantities of genomic DNA from bloodstains on FTApaper processed with the disclosed precipitation method than with thecommercial FTA Purification Reagent system.

EXAMPLE 4

[0215] To demonstrate the general applicability of the presentlydisclosed method of DNA amplification to amplify DNA, a series ofgeneric DNA sequences were used to generate first primers and secondprimers for amplifying genomic DNA. Each DNA sample on FTA paper wasfirst processed using the presently disclosed precipitation method asoutlined in Example 1. Next, the processed DNA samples were amplifiedaccording to the disclosed DNA amplification method, as outlined inExample 2, except that a different set of primers was used in eachreaction. Each set of primers included a second primer as listed below,and a first primer with the same generic sequence as the second primerat its 5′ end and 6 random nucleotides at its 3′ end:5′-ACAACGCAGAGTAAGCAGTGGTA-3′; SEQ ID NO:35′-ACAACGGTAGCAGAGTAAGCAGT-3′; SEQ ID NO:45′-GAGTAAGCAGTACAACGGTAGCA-3′; SEQ ID NO:55′-GAGGCATAAGCAGTACAACGGTA-3′; SEQ ID NO:65′-CAACGGTAGAGGCATAAGCAGTA-3′; SEQ ID NO:75′-GGCATAAGCAGTACAACGGTAGA-3′; SEQ ID NO:85′-AACGGTAGAGGCATAAGCAGTAC-3′; SEQ ID NO:95′-AGTACAACGGTAGAGGCATAAGC-3′; SEQ ID NO:105′-AAGCAGTACAACGGTAGAGGCAT-3′; SEQ ID NO:115′-CGGTAGAGGCATAAGCAGTACAA-3′. SEQ ID NO:12

[0216] For example, in the primer set that included the second primerhaving the sequence of SEQ ID NO: 3, the first primer in the same DNAamplification reaction had the sequence5′-ACAACGCAGAGTAAGCAGTGGTANNNNNN-3′ (SEQ ID NO: 17).

[0217] As shown in FIG. 5., all of the primer sets were able to amplifygenomic DNA from the samples stored on FTA paper. The primer sets usedto amplify the genomic DNA in each lane of FIG. 5. used the followingsecond primer: lane 2, SEQ ID NO: 3; lane 3, SEQ ID NO: 4; lane 4, SEQID NO: 5; lane 5, SEQ ID NO: 6; lane 6, SEQ ID NO: 7; lane 7, SEQ ID NO:8; lane 8, SEQ ID NO: 9; lane 9, SEQ ID NO: 10; lane 10, SEQ ID NO: 11;and lane 11, SEQ ID NO: 12. FIG. 5. demonstrates that a person of skillin the art can design an enormous range of suitable generic sequencesfor first and second primers to amplify DNA according to the presentlydisclosed DNA amplification method in an efficient and uniform manner.

EXAMPLE 5

[0218] The reliability at the nucleotide sequence level of the disclosedmethod of DNA amplification was examined by analyzing PCR amplifiedproducts of a known bovine SNP locus using DNA amplified by thedisclosed method and DNA directly from the FTA paper, similar to thecomparison made in Example 2. In both experiments, the DNA samplesstored on FTA paper were processed using the disclosed precipitationmethod as described in Example 1. Bloodstain samples were collected andstored on FTA paper for 8 individual bovine animals. The FTA papersamples were processed using the disclosed precipitation method, andgenomic DNA was amplified from one set of samples using the disclosedmethod of DNA amplification as described in Example 2. The set ofdehydrated DNA samples and amplified DNA samples were then subjected toPCR amplification as described in Example 2. The PCR products for eachset were subsequently analyzed in a set of Doublecode OLA reactions,which were designed to detect SNP variations among the 8 differentindividual bovine animals.

[0219] Doublecode OLA for SNP detection has been described in U.S.application Ser. No. 09/755,628, incorporated herein by reference, andis illustrated in FIG. 6. As illustrated in FIG. 6., Doublecode OLArequires four different oligonucleotides for SNP detection. A meltingtemperature (Tm) of around 55° C. was used for each of the fouroligonucleotides utilized in the Doublecode OLA. The oligonucleotidesused in the Doublecode OLA method, however, may be of any design thatfacilitates hybridization and the OLA reaction, and are not dependent ona particular Tm. The Tm of an oligonucleotide can be calculated and thelength adjusted accordingly by one of skill in the art using a varietyof computer, software programs, such as Oligo Analyzer, which isavailable at the website www@idtdna.com. All of the oligonucleotides andtheir modifications utilized in Doublecode OLA reactions arecommercially available.

[0220] The first oligonucleotide is an address specific Zipcodeoligonucleotide. The sequence of the Zipcode oligonucleotide is derivedfrom randomly selected nucleotides, and the 5′ end of the Zipcode issubstituted by an amino group with a C₁₂ spacer. A color-coded bead isattached to the 5′ end of the Zipcode oligonucleotide via a couplingreaction catalyzed by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimidehydrochloride (EDC). In one embodiment the color-coded bead is theLuminex color-coded bead. The Luminex color-coded beads have beenspecially modified with carboxyl groups on their surfaces. Carbodiimidecatalyzes the formation of amide bonds between carboxylic acids andamines by activating carboxyl to form an O-urea derivative. Thisderivative reacts readily with nucleophiles, such as amine, to bind theZipcode oligonucleotide to the surface of the bead.

[0221] The second oligonucleotide is a Capture oligonucleotide, which iscomposed of the complementary sequence on the 5′ side of the target SNPplus one of the two SNP nucleotides at its 3′ end. The Captureoligonucleotide is fitted with an AntiZipcode sequence at its 5′ endwhich is the reverse complement of the Zipcode sequence selected above.The AntiZipcode sequence at the 5′ end of the Capture oliogonucleotidewill hybridize with the Zipcode oligonucleotide with a color-coded bead,while the 3′ end of the Capture oligonucleotide will hybridize with aspecific location in the target DNA.

[0222] The third oligonucleotide is the Reporter oligonucleotide, whichis composed of the complementary sequence on the 3′ side (downstream) ofthe target SNP. The Reporter oligonucleotide is fitted with anotherrandomly selected sequence termed the Signalcode at its 3′ end. The 5′end hydroxyl group of the Reporter oligonucleotide is substituted with aphosphate group, which facilitates a ligation reaction catalyzed by Taqligase with the Capture oligonucleotide if the latter anneals perfectlyat its 3′ end with the SNP in the target DNA. The fourth oligonucleotideis the AntiSignalcode oligonucleotide, which is the reverse complementof the random Signalcode sequence selected above. The 3′ end of theAntiSignalcode oligonucleotide is fitted with a biotin that can besubsequently stained by strepavidin-phycoerythrin conjugate.

[0223] Doublecode OLA to detect SNPs in the two sets of PCRamplification products of the 8 different individual bovine wasperformed in a reaction mixture containing the Zipcode oligonucleotide,Capture oligonucleotide, Reporter oligonucleotide, AntiSignalcodeoligonucleotide, and Taq ligase. If the specific SNP designed to bedetected by the oligonucleotides was present in the PCR products, theCapture oligonucleotide was ligated to the Reporter oligonucleotide byTaq ligase, and in a single hybridization reaction simultaneously sortedby the color-coded beads on the Zipcode oligonucleotide as well asstained by a fluor or biotin-labeled AntiSignalcode oligonucleotide. Thefluorescence of the stained bead was measured on a flow cytometer.

[0224] The three ZipCode oligonucleotides used in the reactions were5′-NH₂— (SEQ ID NO:18) 5′-NH2-CGACTCCCTGTTTGTGATGGACCAC-3′; (SEQ IDNO:19) 5′-NH2-CTTTTCCCGTCCGTCATCGCTCAAG-3′; and (SEQ ID NO:20)5′-NH2-GGCTGGGTCTACAGATCCCCAACTT-3′.

[0225] oligonucleotides were coupled to beads according to the followingprocedure. The beads were dispersed in 100 μL of 0.1 M MES (pH 4.5). Theamino-substituted oligonucleotides were added to a final concentrationof 2 μM. Next, 5 μl of freshly made EDC solution(1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrocloride, 100 μg/μl)was added to the reaction and incubated for 20 minutes at roomtemperature in the dark. Addition of the EDC solution and the 20 minuteincubation was repeated. Afterwards, the beads were washed with 0.02%Tween 20 and then 0.1% SDS. The beads were then resuspended in TEbuffer.

[0226] Three Capture oligonucleotides used in the reactions were5′-gtggtccatcacaaacagggagtcgGAAGTCCCAGCTCTGACCTCTCCGG-3′ (SEQ ID NO:21), 5′-cttgagcgatgacggacgggaaaagGAAGTCCCAGCTCTGACCTCTCCGT-3′ (SEQ IDNO: 22), and 5′-aagttggggatctgtagacccagccGAAGTCCCAGCTCTGACCTCTCCGM-3′(SEQ ID NO: 23). The “M” in SEQ ID NO: 23 is the degenerate nucleotidecode for A or C. In the Capture oligonucleotides, the sequence in smallletters is the AntiZipcode sequence and the sequence in capital lettersis the target sequence 5′ upstream of the SNP to be detected. Theoligonucleotides having the sequence of SEQ ID NO: 21 and SEQ ID NO: 22are identical except that the first has the nucleotide G at its 3′ endand the second has the nucleotide T at its 3′ end, which reflect the twoalternate SNP nucleotides located at that position in the bovine genome.The sequence of the Reporter oligonucleotide used was In the Reporteroligonucleotide, the sequence in small letters is the Signalcodesequence and the sequence in capital letters is the target sequence 3′downstream of the target SNP.

[0227] The Doublecode OLA reactions were each carried out in a 20 μlreaction mixture containing: 1×Taq ligase buffer, 0.5 pmol of Captureoligonucleotide, 5.0 pmol of Reporter oligonucleotide with the 5′Signalcode region, and 20 ng of PCR products. The thermocycling programfor the reaction mixtures was 96° C. for 2 minutes, followed by 55cycles of 94° C. for 15 seconds and 37° C. for 1 minute.

[0228] After the thermocycling program was completed, the products weresorted and stained to genotype each of the 8 bovine individuals. TheAntiSignalcode oligonucleotide used to sort the reaction products was5′-ctgaacggtagcatcttgac-biotin-3′ (SEQ ID NO: 24). The sequence of theAntiSignalcode oligonucleotide is reverse complementary to theSignalcode sequence at the 5′ end of the SignalCode Reporteroligonucleotide. The reaction products were simultaneously sorted by thecolor-coded beads on the Zipcode oligonucleotides and hybridized withthe biotinylated AntiSignalcode oligonucleotides in a singlehybridization. These reactions were each carried out in a 50 μlhybridization mixture containing: 1×TMAC buffer (2.5 M TMAC (tetramethylammonium chloride), 0.15% SDS, 3 mM EDTA, and 75 mM Tris-HCl (pH 8.0)),5000 Zipcode oligonucleotides with the color-coded beads for each SNP,2.5 pmol of biotinylated AntiSignalcode oligonucleotides, and 20 μl ofthe Doublecode OLA reaction mixture. The hybridization reaction mixtureswere incubated at 95° C. for 5 minutes and then at 50° C. for 15minutes.

[0229] The hybridized biotinylated AntiSignalcode oligonucleotides werestained with fluorescent strepavidin-phycoerythrin conjugate in areaction that contained 1×TE buffer and the conjugate (10 μg/ml). Thereaction was incubated at room temperature for 5 minutes, and thefluorescent signal of the color-coded beads was measured in a Luminex100 flow cytometer. Table 4 summarizes the genotyping results of DNAsamples processed according to the disclosed precipitation and DNAamplification methods for 8 individual bovine animals. Table 5summarizes the genotyping results of DNA samples processed according tothe disclosed precipitation method only for the same 8 bovine animals.As shown below, both methods give the identical genotype results foreach bovine animal: TABLE 4 1 2 3 4 5 6 7 8 G Bead 26 147 99 31 118 106113 112 T Bead 119 87 106 132 86 188 93 78 A/C Bead 33 40 35 35 26 47 3623 Genotype T G/T G/T T G/T G/T G/T G/T

[0230] TABLE 5 1 2 3 4 5 6 7 8 G Bead 21 140 140 20 137 139 152 132 TBead 176 120 113 138 122 114 103 113 A/C Bead 35 39 36 42 40 32 41 38Genotype T G/T G/T T G/T G/T G/T G/T

[0231] The above results demonstrate that the disclosed method of DNAamplification is able to reliably amplify genomic DNA with highfidelity, which indicates that this method can be used to accuratelygenotype multiple loci within a single organism, even if only a verylimited amount of DNA is available.

EXAMPLE 6

[0232] To further investigate the fidelity of the presently disclosedDNA amplification method, genomic DNA was isolated from the sperm of 8individual bovine animals. The genomic DNA isolated from the sperm wassubjected to PCR amplification using the protocol described in Example2, except that two different primers were used to amplify the DNA:5′-CCAGATTCTTTCGGCAGGTA-3′ (SEQ ID NO: 25), and 5′-CATGGGAACCAGGCTGAAT(SEQ ID NO: 26). The PCR products were sequenced using thedideoxynucleotide chain termination method described by Sanger et al.(Proc Natl Acad Sci USA 74:5463-67, 1977). The genotype for each of the8 bovine individual animals is listed below in Table 6. TABLE 6 1 2 3 45 6 7 8 Genotype T T G T T T G G/T

[0233] Next, genomic DNA isolated from sperm of the same 8 individualbovine animals was subjected to DNA amplification using the disclosedDNA amplification method as described in Example 2. Twenty nanograms ofstarting genomic DNA was amplified. The amplified DNA samples were thensubjected to PCR amplification as described above, and finally the PCRproducts were analyzed in a set of Doublecode OLA reactions, asdescribed in Example 5, which were designed to detect SNP variationsamong the 8 different individual bovine animals. Table 7 summarizes thegenotyping results of the sperm DNA amplified according to the DNAamplification methods of the present disclosure. TABLE 7 1 2 3 4 5 6 7 8G Bead 24 22 227 18 31 21 277 88 T Bead 133 120 35 178 174 93 28 102 A/CBead 31 27 41 37 37 31 24 41 Genotype T T G T T T G G/T

[0234] A comparison of the results in Tables 6 and 7 demonstrates thatDNA products are reliably and consistently amplified from genomicDNA-using the disclosed DNA amplification method. Direct sequencing ofPCR products generated from genomic DNA yield the exact same genotyperesults as Doublecode OLA analysis of PCR products generated from DNAamplified using the DNA amplification method of the present disclosure.These results demonstrate once again that the disclosed method of DNAamplification is able to reliably amplify genomic DNA with highfidelity.

[0235] All of the compositions and methods disclosed and claimed hereincan be made and executed without undue experimentation in light of thepresent disclosure. While the compositions and methods of this inventionhave been described in terms of preferred embodiments, it will beapparent to those of skill in the art that variations may be applied tothe compositions and/or methods and in the steps or in the sequence ofsteps of the methods described herein without departing from theconcept, spirit and scope of the invention. More specifically, it willbe apparent that certain agents that are chemically or physiologicallyrelated may be substituted for the agents described herein while thesame or similar results would be achieved. All such similar substitutesand modifications apparent to those skilled in the art are deemed to bewithin the spirit, scope and concept of the invention as defined by theappended claims.

1 26 1 28 DNA Artificial Sequence modified_base (24)..(28) N = A, G C orT 1 tagcagtggt aacaacgcag agannnnn 28 2 23 DNA Artificial SequenceDescription of Artificial Sequence Synthetic Primer 2 tagcagtggtaacaacgcag aga 23 3 23 DNA Artificial Sequence Description of ArtificialSequence Synthetic Primer 3 acaacgcaga gtaagcagtg gta 23 4 23 DNAArtificial Sequence Description of Artificial Sequence Synthetic Primer4 acaacggtag cagagtaagc agt 23 5 23 DNA Artificial Sequence Descriptionof Artificial Sequence Synthetic Primer 5 gagtaagcag tacaacggta gca 23 623 DNA Artificial Sequence Description of Artificial Sequence SyntheticPrimer 6 gaggcataag cagtacaacg gta 23 7 23 DNA Artificial SequenceDescription of Artificial Sequence Synthetic Primer 7 caacggtagaggcataagca gta 23 8 23 DNA Artificial Sequence Description of ArtificialSequence Synthetic Primer 8 ggcataagca gtacaacggt aga 23 9 23 DNAArtificial Sequence Description of Artificial Sequence Synthetic Primer9 aacggtagag gcataagcag tac 23 10 23 DNA Artificial Sequence Descriptionof Artificial Sequence Synthetic Primer 10 agtacaacgg tagaggcata agc 2311 23 DNA Artificial Sequence Description of Artificial SequenceSynthetic Primer 11 aagcagtaca acggtagagg cat 23 12 23 DNA ArtificialSequence Description of Artificial Sequence Synthetic Primer 12cggtagaggc ataagcagta caa 23 13 23 DNA Bovine 13 ccttttcctc tagcatcaagtta 23 14 21 DNA Bovine 14 cagactgtgt gcttcctaca g 21 15 21 DNA Bovine15 ccagcagttc tgaatgaaag t 21 16 18 DNA Bovine 16 acacacagag gccgtgta 1817 29 DNA Artificial Sequence Description of Artificial SequenceSynthetic Primer 17 acaacgcaga gtaagcagtg gtannnnnn 29 18 25 DNAArtificial Sequence Description of Artificial Sequence Synthetic Primer18 cgactccctg tttgtgatgg accac 25 19 25 DNA Artificial SequenceDescription of Artificial Sequence Synthetic Primer 19 cttttcccgtccgtcatcgc tcaag 25 20 25 DNA Artificial Sequence Description ofArtificial Sequence Synthetic Primer 20 ggctgggtct acagatcccc aactt 2521 49 DNA Bovine 21 tggtccatca caaacaggga gtcggaagtc ccagctctgacctctccgg 49 22 50 DNA Bovine 22 cttgagcgat gacggacggg aaaaggaagtcccagctctg acctctccgt 50 23 49 DNA Bovine 23 aagttgggga tctgtagacccagccgaagt cccagctctg acctctccg 49 24 20 DNA Artificial SequenceDescription of Artificial Sequence Synthetic Primer 24 ctgaacggtagcatcttgac 20 25 20 DNA Bovine 25 ccagattctt tcggcaggta 20 26 19 DNABovine 26 catgggaacc aggctgaat 19

What is claimed is:
 1. A method of amplifying DNA, the methodcomprising: (a) providing a single reaction mixture comprising: (i) aDNA sample; (ii) a first primer comprising a random sequence ofnucleotides at its 3′ end and a generic sequence 5′ of the randomnucleotides; and (iii) a second primer comprising the generic sequenceof the first primer and lacking the random sequence of the first primer;(b) subjecting the DNA sample to DNA amplification by a first DNApolymerase wherein the first primer anneals to the DNA to allow thefirst DNA polymerase to produce a DNA product; and (c) subjecting theDNA product of step (b) to DNA amplification by a heat-stable DNApolymerase wherein the second primer anneals to the DNA product.
 2. Themethod of claim 1, wherein the DNA amplification of step (b) comprisesthe steps of denaturing the DNA product; annealing the first primer withthe DNA to allow the formation of a DNA-primer hybrid; and incubatingthe DNA-primer hybrid to allow the first DNA polymerase to synthesize aDNA product.
 3. The method of claim 2, wherein the DNA amplificationsteps are repeated at least one time.
 4. The method of claim 1, whereinthe DNA amplification of step (c) comprises the steps of denaturing theDNA product; annealing the second primer with the DNA product to allowthe formation of a DNA-primer hybrid; and incubating the DNA-primerhybrid to allow the heat-stable DNA polymerase to synthesize a secondDNA product.
 5. The method of claim 4, wherein the second DNA product isflanked by the generic sequence and reverse complement of the genericsequence.
 6. The method of claim 4, wherein the annealing temperature ishigher than the optimal annealing temperature of the random sequence ofnucleotides of the first primer.
 7. The method of claim 4, wherein theDNA amplification steps are repeated about 30 to about 40 times.
 8. Themethod of claim 1, wherein the first DNA polymerase has 5′ to 3′exonuclease activity.
 9. The method of claim 1, wherein said first DNApolymerase has primer displacement activity.
 10. The method of claim 1,wherein the heat-stable DNA polymerase is Taq DNA polymerase.
 11. Themethod of claim 1, wherein the first DNA polymerase and the heat-stableDNA polymerase are the same DNA polymerase.
 12. The method of claim 1,wherein the first primer comprises about 4 to about 8 random nucleotidesat its 3′ end.
 13. The method of claim 1, wherein the generic sequenceof the first primer is about 15 to about 28 nucleotides in length. 14.The method of claim 1, wherein the random nucleotides of the firstprimer are G:C rich.
 15. The method of claim 1, wherein the randomnucleotides of the first primer are A:T rich.
 16. The method of claim 1,wherein the generic sequence of the first primer comprises a single ormultiple restriction enzyme recognition site.
 17. The method of claim 1,wherein the DNA sample is selected from the group consisting of genomicDNA, microdissected chromosome DNA, yeast artificial chromosome (YAC)DNA, cosmid DNA, phage DNA, P1 derived artificial chromosome (PAC) DNA,and bacterial artificial chromosome (BAC) DNA.
 18. The method of claim1, wherein the DNA sample is selected from the group consisting ofmammalian DNA, plant DNA, yeast DNA, viral DNA, and prokaryotic DNA. 19.The method of claim 1, wherein the DNA sample is obtained from a human,bovine, porcine, ovine, equine, rodent, avian, fish, shrimp, plant,yeast, virus, or bacteria.
 20. The method of claim 1, wherein the DNAsample is bovine DNA.
 21. The method of claim 1, wherein the DNA sampleis tissue on a solid medium.
 22. The method of claim 1, wherein the DNAsample is obtained from a buccal swab, a nose swab, blood, cord blood,amniotic fluid, embryonic tissue, hair, endothelial cells, hoofclippings, or fingernail clipping.
 23. The method of claim 1, furthercomprising genotype analysis of the amplified DNA product.
 24. Themethod of claim 1, further comprising identifying a single nucleotidepolymorphism (SNP) in the amplified DNA product.
 25. The method of claim24, wherein the SNP is identified by Oligonucleotide Ligation Assay(OLA), Doublecode OLA, sequencing, Single Base Extension Assay, allelespecific primer extension, or mismatch hybridization.
 26. A method ofamplifying DNA, the method comprising: (a) providing a single reactionmixture comprising: (i) a DNA sample; (ii) a first primer comprising arandom sequence of nucleotides at its 3′ end and a generic sequence 5′of the random nucleotides; (iii) a second primer comprising the genericsequence of the first primer and lacking the random sequence of thefirst primer; and (iv) a heat-stable DNA polymerase; (b) subjecting theDNA sample to DNA amplification wherein the first primer anneals to theDNA to allow the heat-stable DNA polymerase to produce a DNA product;and (c) subjecting the DNA product of step (b) to DNA amplificationwherein the second primer anneals to the DNA product.
 27. The method ofclaim 26, wherein the heat-stable DNA polymerase is Taq DNA polymerase.28. The method of claim 26, wherein the DNA amplification of step (b)comprises the steps of denaturing the DNA product; annealing the firstprimer with the DNA to allow the formation of a DNA-primer hybrid; andincubating the DNA-primer hybrid to allow the heat-stable DNA polymeraseto synthesize a DNA product.
 29. The method of claim 28, wherein the DNAamplification steps are repeated at least one time.
 30. The method ofclaim 26, wherein the DNA amplification of step (c) comprises the stepsof denaturing the DNA product; annealing the second primer with the DNAproduct to allow the formation of a DNA-primer hybrid; and incubatingthe DNA-primer hybrid to allow the heat-stable DNA polymerase tosynthesize a second DNA product.
 31. The method of claim 30, wherein theannealing temperature is higher than the optimal annealing temperatureof the random sequence of nucleotides of the first primer.
 32. A methodof identifying a polymorphism, the method comprising: (a) providing asingle reaction mixture comprising: (i) a DNA sample; (ii) a firstprimer comprising a random sequence of nucleotides at its 3′ end and ageneric sequence 5′ of the random nucleotides; and (iii) a second primercomprising the generic sequence of the first primer and lacking therandom sequence of the first primer; (b) subjecting the DNA sample toDNA amplification by a first DNA polymerase wherein the first primeranneals to the DNA to allow the first DNA polymerase to produce a DNAproduct; (c) subjecting the DNA product of step (b) to DNA amplificationby a heat-stable DNA polymerase wherein the second primer anneals to theDNA product to allow the heat-stable DNA polymerase to produce amplifiedDNA products; and (d) analyzing the amplified DNA products of step (c)to identify a polymorphism.
 33. The method of claim 32, wherein thepolymorphism is a single nucleotide polymorphism (SNP).
 34. The methodof claim 33, wherein the SNP is identified by Oligonucleotide LigationAssay (OLA), Doublecode OLA, sequencing, Single Base Extension Assay,allele specific primer extension, or mismatch hybridization.
 35. Amethod of amplifying DNA, the method comprising: (a) providing areaction mixture comprising: (i) a DNA sample to be amplified; (ii) afirst primer comprising a random sequence of nucleotides at its 3′ endand a generic sequence 5′ of the random sequence; and (iii) a secondprimer comprising the generic sequence and lacking the random sequenceof the first primer; (b) heating the reaction mixture to a temperaturethat denatures the DNA to be amplified; (c) cooling the reaction mixtureto a temperature that allows the random sequence of the first primer tohybridize to its complement DNA and incubating the reaction mixture toallow synthesis of a DNA product by a DNA polymerase; (d) repeatingsteps (b) and (c) at least one time; and (e) performing a series of DNAamplification reactions wherein the annealing step is at a temperaturethat selects for the generic sequence of the second primer hybridizingto complement DNA in the DNA product over the random sequence of thefirst primer hybridizing to complement DNA in the DNA product.
 36. In amethod for amplifying a DNA sample on a solid medium, the improvementcomprising precipitating the DNA sample on the solid medium andsubjecting the precipitated DNA to DNA amplification to produceamplified DNA products.
 37. The method of claim 36, wherein the solidmedium is filter paper.
 38. The method of claim 37, wherein the filterpaper is chemically treated.
 39. The method of claim 37, wherein the DNAsample is dehydrated on the filter paper.
 40. The method of claim 36,wherein the DNA sample is precipitated with salt and alcohol, and rinsedwith alcohol.
 41. The method of claim 40, wherein the salt is selectedfrom the group consisting of sodium acetate, potassium acetate, ammoniumacetate, sodium chloride, and potassium chloride.
 42. The method ofclaim 40, wherein the alcohol is ethanol or isopropanol.
 43. A method ofidentifying a polymorphism, the method comprising: (a) precipitating aDNA sample on a solid medium; (b) providing a single reaction mixturecomprising: (i) the DNA sample; (ii) a first primer comprising a randomsequence of nucleotides at its 3′ end and a generic sequence 5′ of therandom nucleotides; and (iii) a second primer comprising the genericsequence of the first primer and lacking the random sequence of thefirst primer; (c) subjecting the DNA sample to DNA amplification by afirst DNA polymerase wherein the first primer anneals to the DNA toallow the first DNA polymerase to produce a DNA product; (d) subjectingthe DNA product of step (c) to DNA amplification by a heat-stable DNApolymerase wherein the second primer anneals to the DNA product to allowthe heat-stable DNA polymerase to produce a second DNA product; and (e)analyzing the second DNA product to identify a polymorphism.
 44. Themethod of claim 43, wherein the DNA sample is precipitated with salt andalcohol, and rinsed with alcohol.
 45. A method of amplifying DNA, themethod comprising: (a) providing a reaction mixture comprising: (i) aDNA sample; (ii) a first primer comprising a random sequence ofnucleotides at its 3′ end and a generic sequence 5′ of the randomnucleotides; and (iii) a second primer comprising the generic sequenceof the first primer and lacking the random sequence of the first primer;(b) subjecting the DNA sample to DNA amplification by a first DNApolymerase wherein the first primer anneals to the DNA to allow thefirst DNA polymerase to produce a DNA product; and (c) subjecting theDNA product of step (b) to DNA amplification by a heat-stable DNApolymerase wherein the second primer anneals to the DNA product.
 46. Amethod of amplifying DNA, the method comprising: (a) providing areaction mixture comprising: (i) a DNA sample; (ii) a first primercomprising a random sequence of nucleotides at its 3′ end and a genericsequence 5′ of the random nucleotides; (iii) a second primer comprisingthe generic sequence of the first primer and lacking the random sequenceof the first primer; and (iv) a heat-stable DNA polymerase; (b)subjecting the DNA sample to DNA amplification wherein the first primeranneals to the DNA to allow the heat-stable DNA polymerase to produce aDNA product; and (c) subjecting the DNA product of step (b) to DNAamplification wherein the second primer anneals to the DNA product.